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The world of the Teenage Mutant Ninja Turtles is a Near-Earth setting, but while histories don't diverge until modern day, there's a blip in the past that sets all of that into motion. Roughly 2 million years ago, when primates had evolved into Homo Erectus, an alien race of "brains with tentacles" called the Kraang decided that Earth was their #1 Real Estate pick for expanding their territory. Dimension travel is one thing, but sustainable living is another, because the Kraang had to enact a 2 million year-long genome project on the Homo Erectus species just to create a being that was "uniquely attuned to this dimension" and use that being for the Kraang terraforming of Earth. The Kraang thus used the first round of their Mutagen ( http://turtlepedia.wikia.com/wiki/Mutagen_%282012_TV_series%29 ) and turned Homo Erectus into Homo Sapiens. Little examples survived throughout history of the Kraang checking in on the progress of their experiment in either regular alien form or their Kraangdroid human-esque bodies ( http://turtlepedia.wikia.com/wiki/Kraang_%282012_TV_series%29/Gallery ) - carvings, paintings, etc. - but the history we're familiar with remained intact.
Roughly 16 years before "present" (2012-ish), a much more human conflict came to a head. Hamato Yoshi and Oroku Saki were raised together, although Oroku Saki had been stolen from the Foot Clan as a baby. While the two had always been brotherly rivals, their mutual affection for a girl named Tang Shen tore them apart. In Saki's eyes, Yoshi stole Tang Shen from him. Angry words were said and the two men parted ways no longer friends. Hamato Yoshi and Tang Shen were married, and a daughter came into their lives: Miwa. But Saki chose to have vengeance over friendship, and he returned to burn Yoshi's life to the ground. In the chaos, Saki attacked Yoshi personally, and a blow that was meant for Yoshi struck Tang Shen. Once again, Saki blamed Yoshi for stealing Tang Shen from him, and so he stole Miwa - away from Yoshi's eyes, so that he believed her to be dead, just like Tang Shen.
During Yoshi's bereavement, he made the decision to move to New York City. One day, after he went to the pet store and picked up four baby turtles, the two strings of fate became tangled. Hamato Yoshi happened to walk a Kraangdroid, and the man seemed unusual, so he followed the man into an alleyway where TWO of the same man - as all Kraangdroids are manufactured the same way - were conversing while holding a canister of Mutagen. Having been discovered, the Kraangdroids attacked along with two of their nearby fellows, and Yoshi defended himself. He knocked the Mutagen out of their hands and won the fight, but because the Mutagen was spilled and he dropped the glass bowl holding the turtles, the five of them were all changed. Hamato Yoshi became more animalistic, morphing into an anthropomorphic rat and began calling himself "Splinter" instead. The four turtles became more human, and Splinter chose to adopt them as his sons, calling them "the unlikeliest of families" - but a family nonetheless. He named the four turtles after his favorite painters and sculptors from the Renaissance: Leonardo, Raphael, Donatello, and Michelangelo.
During the next 15 years, the four turtles never went above the surface. Splinter helped them acquire some human paraphernalia along the way to furnish their lair with, and weapons to train with, etc., but for Leonardo in particular nothing impacted him as much as discovering the television show Space Heroes - an animated parody of Star Trek: The Animated Series. The character of Captain Ryan - aka Captain Kirk - became a role model for Leonardo, and he aspired to be as great a hero before he became the formal leader of the turtles. Leonardo learned a lot of scattered Japanese phrases and form names in that time, as well as calligraphy. He took Splinter's teachings to heart, not just his fighting techniques, and is officially the oldest of the four, being the Big Brother to all three of the other turtles. Michelangelo became the family cook and they survived mostly on worms & algae all those years, training in ninjutsu day in and day out - unless they were skating together through the sewers or playing each other on their arcade games in the lair.
-SEASON ONE- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_1%29
On their 15th Mutation Day, Leonardo asked for what the other three turtles must have discussed at length beforehand: to go up on the surface and explore. Reluctantly, Splinter agreed, and they discovered - among other things - the almighty pizza. Oh and April O'Neil getting kidnapped by the Kraang. Of course, the turtles didn't know it was the Kraangdroids, they just tried to fight them off and lost because they couldn't fight as a team. Trying to regroup, Splinter agreed they needed a leader and Leonardo asked for the position. So granted, Leonardo decided they need to stake out a building in hopes of finding April's kidnappers, which worked after a fashion. In the struggle, another canister of Mutagen rolled out of the van used to take her away. The lone human kidnapper was Snake, who told them the group was called "The Kraang". Unfortunately, Mikey let Snake escape; fortunately, Leonardo and Raphael silently agreed to discuss their plan in front of a hiding Snake so that they'd prepare for the wrong kind of attack. Back at the lair, Leonardo solidified their true plan with a pep talk from Splinter while Donatello made them climbing gear. They snuck into the Kraang's satellite facility and and discovered the Kraang's identity as aliens in robot bodies. They rescued April and defeated a mutated Snake (plant hybrid now called Snakeweed by Mikey), but a small force of Kraang escaped with April's father. The four turtles dropped April off at her aunt's place and promised to help her reunite with her father, then returned to the lair. Leonardo found out that the reason Splinter made him leader was because he asked to be, and that choices wouldn't always be right or wrong. Leo had to realize he wouldn't be a leader immediately, but learn how to become a good one. A news report on the incident - "Ninjas in New York" - reached Oroku Saki all the way in Japan, where he recognized the Hamato crest on a recover shuriken. Oroku Saki had become Shredder, the leader of the Foot Clan he was a part of by birth, and decided to fly to New York to destroy his old nemesis. Thus the world-threat of the Kraang intersected with the personal vendetta of the Shredder, even if the turtles didn't know it yet.
Each of the turtles had their own personal flaws to work on and the next several episodes were devoted to that. Raphael's temper almost got the turtles exposed to the whole world, and then Michelangelo's good faith in people enabled him to befriend Shredder's star pupil, Chris Bradford. The turtles successfully thwarted Bradford and his Foot ally, Xever, using teamwork and identifying the need to switch opponents mid-combat, but Splinter warned the boys that the fight was only beginning. For Leonardo, his problem was that he didn't command enough respect to just issue orders his brothers would follow. By trying to stick with brothers as family, they got into more trouble and created an enemy for themselves in Baxter Stockman, which escalated with the help of some tech Donatello created and Baxter acquired thanks to Mikey's negligence. They finally came clean with Splinter, regrouped, and defeated Baxter, but Leonardo would need a lot more experience before his brothers would respect him. Likewise, he had to understand that being a Leader would mean making unpopular decisions. Splinter advised that they look deeper into their ninja training for the secret to fighting someone in armor, and Leonardo took that lesson to heart as well. While fighting the Kraang, Donatello became disheartened about his ability to fight with his bo staff, and successfully created a robot drone called Metalhead that Donatello could control with a video-game remote. April discovered a Kraang plot to pollute the water supply of NYC, so Donatello used Metalhead during the ensuing fight. Unfortunately, since Metalhead was created from Kraang tech, a Kraang was able to take it back over, and Donatello had to defeat his own drone after joining his brothers in person. For as intelligent as Donatello is, he was struggling with everyday wisdom.
The turtles had to fight a mind-reading ally of the Kraang called Doctor Falco, and during that time Shredder descended upon NYC. He put Xever in charge, bringing Xever's allies the Purple Dragons into the fight. The turtles discovered them roughing up a blind restaurant owner, Mr. Murakami, and Leonardo showed the leader Fong mercy. Raphael gave Leo a really hard time about it, but later on Murakami got kidnapped by Xever and the Purple Dragons. When the turtles were about to be defeated by Xever and Bradford, Fong returned Leonardo's sword to him, and they managed to escape. Leo learned that mercy wasn't a weakness, and Splinter's other lesson about seeking victory not fairness was also highly relevant. The Kraang and Shredder's plots converged accidentally when they got a chance to rescue April's father, but the effort only resulted in discovering the Kraang were planning to detonate a mutagen bomb over the city. Xever and Bradford attacked the turtles while Donatello was trying to diffuse the bomb. Donatello was successful, but rather than fail the Shredder again, Bradford tried to unleash the mutagen on the six combatants so they'd all perish together. Instead, Xever was turned into a barracuda hybrid called Fishface and Bradford himself became a dog hybrid mutant called Dogpound. Shredder himself attacked the turtles and they barely escaped with their lives, which shot their confidence down immensely and made Splinter panic for fear of losing his second family. He made the turtles train hard for weeks before permitting them to surface again.
What finally brought them up again was a plot from Shredder to destroy their lair in the sewers, even if he didn't know the exact location. The turtles fought the newly mutated Dogpound and lost, furthering their own fear, but April still had enough courage to uncover Shredder's plan. The brothers fought Dogpound again and won, saving the lair, and Splinter apologized for inciting the panic. Like many young people learning powerful skills, Leo and Raph got over-confident in their abilities as compared to Donnie and Mikey, and when the four decided to strike against the Purple Dragons for stealing from April, they split up into "A Team" and "B Team" - very much against Donatello and Michelangelo's wishes. A brotherly spat brought out into the streets got them mixed up in an alliance between Dogpound and Baxter Stockman. Leo and Raph were left outrunning Baxter's Mousers, trying to fend off a relentless robot army to the point of exhaustion. Only once Leo and Raph rejoined with Donnie and Mikey were the two groups able to defeat their individual foes together AND they really shouldn't have instigated the fight in the first place.
The Kraang lost control of a captive alligator mutant who eventually became their ally thanks to Mikey's compassion, and he named him Leatherhead. The brothers took a Kraang power cell into their protection at Leatherhead's request, to keep it safe so the Kraang didn't use it to power their portal to Dimension X. The turtles escaped the Kraang by powering a train car with the power cell, which Donatello turned into the Shellraiser vehicle. Dr. Victor Falco returned as a rat hybrid mutant after a spill in his makeshift lab, and even managed to use his mind-control powers on Splinter himself. Together, the four turtles had to defeat their father (who wasn't holding back now like in their training sessions) without seriously injuring him. Leonardo used Splinter's picture of himself as Hamato Yoshi with his wife and daughter to remind him who he was, and called out to him as father, which brought Splinter out of The Rat King's control so Splinter could deal the finishing blow.
Raphael had gotten on Leonardo's case before about his chosen methods for leading the brothers during battle, but not as rough as when Snakeweed reappeared and kidnapped someone. Leo snapped and told Raph he could lead since he thought he could do it better, and when Leo went to blow off some steam, the Foot Clan attacked. That was when Karai found him, a female ninja better than the nameless Foot warriors. She toyed with him and let him go, leaving him to rest back at the lair while his brothers went out on a mission. Splinter found out that Leo shucked his responsibility, with Leo whining that his brothers didn't understand the pressure he was under, and that they didn't appreciate him. Splinter told his son "it doesn't matter if the burden is heavy, only that you carry it." Of course, it didn't sink in right away. Leo was tasked with catching up to the other turtles, but Karai waylaid him. She told him to meet her at the Byerly building at midnight, so Leonardo went to April for advice, who promptly scolded him - physically and verbally - for hanging out with a member of the Foot Clan. Leo insisted she was different, but April wasn't convinced, and asked only that he be careful. Just to be safe, she told Donatello where Leo was heading. Meanwhile, the trio of brothers wasn't faring so well, with Raph freezing up at trying to make decisions that would risk his brothers' lives fighting Snakeweed. Donnie helped Raph get Mikey home safe - but Leo wasn't there or with them, a fact Splinter noticed immediately. While Raphael now understood Leonardo's position, they still had to find him. Thanks to Donatello's text from April, Raphael knew where to find Leo, but Raph also caught him in the middle of talking to Karai. Karai was trying to convince Leo to steal the sword of Miyamoto Musashi, but Leo refused, so Karai pinned Leo to the top of the building - only Leo didn't sound too upset about it when Raph found them. Snakeweed tracked Raphael down and with indirect help from Karai, the two brothers defeated Snakeweed after a rare verbal apology from Raphael. Leo had to tease him about that a bit, but ultimately they reconciled, and Leo kept right on crushing on Karai too.
That's why Raphael kept close tabs on Leonardo when he started showing off during a fight. He kept trying to convince Leo otherwise, but Leonardo wouldn't give up thinking Karai had a good side to her. He waited for her alone on a rooftop, and the fought again until she ran off again. Leo warned her that "if you come after them, I'll come after you." An improved Kraangdroid sent by one of the Kraang's shell organization "The Worldwide Genome Project" attacked April and the turtles tracked it down after rescuing her, but Karai followed them. Donatello and Mikey found out the backstory mid-combat, right before Karai jumbled a bunch of DNA into a giant Mutagen canister and created a monster, then just left the fight. Leonardo felt betrayed initially, but ultimately took responsibility for allowing Karai to get involved - and for being blinded by his attraction to her. He came clean to his family and to April, and insisted he'd give up liking her, but such things are easier said than done. Leonardo's mistake also helped Karai bring a piece of Kraang technology to the Shredder's doorstep, which would prove costly as it ultimately led to Shredder allying himself with the Kraang. The next of Shredder's alliances the turtles discovered was with Baxter Stockman, which was how Xever's Fishface form became land-compatible again.
Since the turtles were using the Kraang's power cell for their Shellraiser vehicle, it was only a matter of time before Donnie's defensive mechanisms on it failed. The Kraang got it back and when they couldn't retrieve it, they confessed to Leatherhead about losing it. Eventually, Leatherhead calmed down enough to tell them the repercussions of the Transporter being operational - that the Kraang could bring things from Dimension X again, namely backup forces. He remembered and drew a honeycomb-like symbol for them to help them find the building, which they eventually figured out was for TCRI - another shell organization like the WWGP. With April and Leatherhead's help, they sneaked into the TCRI building and even got all the way to the top floors, but the Kraang had filled the upper floors with noxious atmosphere from Dimension X and the turtles passed out from lack of oxygen. When they woke up, they were captured, and had to fend off the Kraang while holding their breaths. Leatherhead sacrificed himself to try shutting down the portal from the other side, leaving the turtles to escape the building and unfortunately with the portal intact. However, they did find out one of the Kraang's ultimate objectives: April, not her father. Donatello tried to help them spy on the Kraang with a cockroach, but the roach ended up mutating during its mission, leaving the turtles to both stop the Kraang's plot to drill through the Earth's crust AND stop the mutant roach at the same time. It didn't help that Raphael has a roach phobia, which he confronted but didn't get over during the fight with Donatello's roach.
Both Shredder's forces and the turtles went after the Kraang's newest weapon - the Spacial Endal Particle Disruptor - and ended up disrupting each others' efforts. Baxter took the fall for the blunder so that he could try to get the turtles plus Dogpound and Fishface all in the same gambit, but the turtles managed to make a temporary truce with Shredder's henchmen and survive Baxter's maze of lethal traps. Karai tried to get the same chance, but understandably Leo's three brothers were incredibly resistant to the idea. Leonardo believed her and Karai suggested they steal one of several missile launchers from a shipment that Shredder was receiving. To test her, they made her get it herself, but ended up doubling back on the promise to team up against the Kraang for the opportunity to take down Shredder. In the ensuing threeway battle with Shredder and a Kraang scout ship, Karai told Leonardo Shredder was her father, and the fight ended in a standstill between the Foot Clan and the turtles. Leonardo did manage to shoot down the Kraang ship with the missile launcher, but still felt bad for losing their chance to have Karai as an ally. In fact, Karai took the next opportunity to target April specifically while the guys took a mini-sub Donnie made to the bottom of the East River, trying to destroy another remote Kraang facility that was polluting the water supply with Dimension X water. After that, Splinter suggested - and Leo agreed - that with both Shredder's forces and the Kraang after April, she should live with them in the sewers for awhile.
In desperation to have a stronger army, Shredder contracted with the Kraang to create an army. Their first plot was to mutate existing human Foot Ninjas, which led to their incompetent human ally The Pulverizer (Timothy) becoming a mole despite Donatello's hesitation. At the same time, Splinter insisted the turtles learn different fighting styles. Leonardo ended up with Donatello and Mikey got Leo's swords. They didn't last one fight before Leo suggested they switch back - one of the few times Leo went against Splinter's lesson, thinking it was to help them all stay alive. Splinter wasn't amused and took their weapons away instead to teach them resourcefulness. During the fight, Timothy insisted on trying to become a mutant to be more awesome, but only succeeded in turning into a blob. The defeat solidifed an alliance between the Kraang and Shredder, leading to the development of FootBots - robot ninjas with Foot Clan training, but bodies made similar to the Kraangdroids. Another experiment in the FootBot development was on a wasp that stung Leonardo, turning him into a drone protector for the mutant's eggs that could infect others zombie/werewolf-style. He succumbed and turned his brothers while defending the egg, but Michelangelo saved them by completing an antidote Donatello developed.
Donatello decrypted a secret message from April's father, but it was a Kraang trap to get the turtles to take Kirby O'Neil back with them so he could find April. In actuality, Kirby was being mind-controlled by the Kraang so that he'd turn April over to the Kraang. While Donatello managed to break Kirby out, they also unleashed a Kraang captive criminal dubbed Newtralizer. They defeated the Newtralizer while April found a Kraang communication orb, which helped alert the turtles that the Kraang were planning to start their invasion by bringing in a tank-like fortress called the Technodrone from Dimension X.
Splinter advised Leonardo that there may be a need for sacrifices in the upcoming battle, with the fate of the world at hand. With the turtles away, Mind-Controlled Kirby managed to lead April away from the lair and into Karai's hands. April was used as bait for Splinter to fight Shredder while the turtles attacked TCRI with their full strength, the primary goal being to knock out the portal before the Technodrone could come through. Metalhead was sent in first while the turtles descended on the upper levels of TCRI on gliders. The Kraang's SEPD gun might have destroyed the portal, but it had a forcefield around it. Splinter fought Shredder and nearly defeated him, except Karai interfered and Splinter was disheartened to learn she was his daughter Miwa - alive, but raised by Shredder. The Kraang managed to bring the Technodrone to NYC despite the turtle's best efforts, namely involving Leonardo jumping out of the building at the end of a failed blow-it-all-up gambit. Raphael was the one to save him from splattering on the streets. The turtles regrouped back at the lair thinking they could get Splinter's and April's help, but they had to get Kirby un-mind-controlled first. Kirby then explained April would be in the Technodrone by now, so the turtles plotted to sneak in. They succeeded but Kraang Prime came after them so as not to lose the precious Uniquely Attuned Mental Energy that the Kraang had been engineering for so long. Leonardo was able to hold Kraang Prime back long enough to send the Technodrone crashing into the water, but ordered his brothers to take April and escape without him. He dove out at the last second, but scared his brothers long enough they thought he'd died. They celebrated their victory, thinking Shredder and the Kraang were defeated, but it was short-lived.
-SEASON TWO- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_2%29
The turtles still had the Kraang communication orb, and realized that the Kraang were regrouping. They went after a Kraang stealth ship that was delivering mutagen to the Shredder, but ended up dumping canisters all over the city. Among the people affected by the rain of mutagen canisters was Kirby O'Neil and when the boys tried to take responsibility for the accident, April shunned them. The rest of the season primarily used Donatello's tracking devices to locate the canisters and the beings affected by them. First up were mutant squirrels that doubled inside of a person's gut.
As the hunt wore his brothers down, Leonardo suggested they take a break for a training session. Leo had to defend a gate against each of his brothers in turn, but they used their own styles of fighting to get past him. Leonardo took it as an insult, but Splinter advised him that a leader didn't always have to impose their will on their followers. While that was true, the other side to the advice was helping his followers flourish - and thereby earning their respect. Because the brothers didn't listen to Leonardo's orders and wouldn't retreat when he told them to, they were ambushed by the new FootBots in their first fight against them. When Mikey got in trouble, Leo leaped down to save him, but was captured in the process. Raphael, Donatello, and Michelangelo went to rescue Leonardo while Karai insisted this was her vengeance for Splinter taking her mother away. Leo denied that Splinter would do such a thing, but Leo was just bait for the other turtles, and eventually for Splinter himself. However, the four brothers escaped, and Leonardo ended up coming around to the idea of being unpredictable - and slightly unconventional - as a valid fighting technique. Leo defeated Karai and told her that her grudge was misplaced, then they escaped with a smokebomb. Back at the lair, Raphael even apologized, but Leo had to ask Splinter about what Karai accused Splinter of doing. That was when Splinter told Leonardo - and him alone - that Karai was in fact his daughter. Leonardo kept his father's secret for him and didn't tell his brothers.
Later, Timothy tried to fix his mutated state by drinking more mutagen, only to become Mutagen Man, but the turtles froze him in order to stop him, much to Donatello's regret. Next, Mikey nearly exploded from over-exposure on his skin for starters. Two things happened at that time, Dogpound mutated a second time into Rahzar and, after the turtles escaped, Donatello started to develop some anti-mutagen serum in order to reverse Mikey's "Shellacne" condition. Unfortunately, April needed some time to forgive the turtles for the accident not being their fault. Karai tried to commission a special Kraangdroid to kidnap April, but they turned on her and tried to capture April for themselves. It reunited April with the turtles, but it also introduced Casey Jones to the picture as he helped defend April from the FootBots Karai sent after her.
Another victim of the mutagen this season was Raphael's pet snapping turtle, Spike, who transformed into a mutant turtle himself and started going by "Slash." At first, Raphael was delighted to have a new brother, until Slash decided that the best way to free Raphael from the chains holding him back (from becoming a 24/7 crime-fighter) was to eliminate the brothers he professed to hate so much. Leonardo went on a stealth mission alone to recover a mutagen canister, not realizing that Slash had beaten Donatello and Michelangelo within an inch of their lives. While Raphael fended Slash off, Leonardo ended up having a tea party with a little girl (seriously) until the two raging turtles came crashing through her wall. Together, Raphael and Leonardo managed to fend him off until he went over the edge of a building. It didn't kill Slash, but it did send him running and encouraged Raphael to cherish his brothers a little more.
It was after Slash's attack that Raphael discovered Casey going vigilante as well, but too extreme even for Raphael. As a result of one of Raph's tantrums, Casey was able to track him back to their lair, and FootBots were able to track Casey. They barely managed to destroy all of the FootBots before they could report on the lair location. Raphael and Casey had to work together to take down a runner, coming to a mutual understanding in the process.
Soon enough, the turtles learned how deep the Kraang's plot ran - centuries old and very clearly engineering human DNA to create April's specific strain. Thanks to a journalist called Kurtzman, they also realized that the Kraang had already rebuilt TCRI. They wanted to sneak in without April and wipe out the records the Kraang had of April's DNA in order to keep her safe, but April joined them anyway. April was able to overhear Kraang Prime talking to her subordinates, leading to her capture within the TCRI building. Raphael rescued her while Leonardo, Donatello, and Michelangelo fought off April Clones, including a disfigured one that was very strong. Just when April was about to be hurt by the Kraang's devices, she let out a sonic scream-like attack. Back in Donnie's lab, they discovered why - the "specific string of DNA" April has is that of a half-human half-alien mutant. April of course took it harder than the guys did, but it solidified their family unit bond with her and goal to keep her safe from the Kraang.
Leonardo started having recurring nightmares where he failed his brothers and they were dragged off into darkness. A mutant fungus attack made him confront them as their spores caused fear-based hallucinations. For Leonardo, his hallucination also included his brothers saying how he'd let them down. He meditated mid-combat long enough to remind himself he faced his fear every day, and exposed the fungus to sunlight, thus destroying it.
Donnie managed to rewire Metalhead with an AI, but his first mission with them became his last too. The turtles discovered the Kraang capturing Mutants in order to control them the way they did Kirby O'Neil at the end of Season 1. Metalhead managed to open the portal again, but could only keep it open manually. To get the turtles home again through the same portal, Metalhead had to stay behind and hold the portal open. Metalhead self-destructed, but his head blew up through the portal for Donatello to recover. The Rat King tried to make a combat but was thwarted, during which time Shredder returned from a trip to Asia with a new ally - Tiger Claw, a mutant assassin from Asia.
Since Splinter told Leonardo that Karai was his daughter Miwa, Leonardo tried to tell Karai as well, but failed because a localized earthquake interrupted the fight. Leonardo at least convinced Splinter to tell his brothers about their "sister." While they processed that information, Casey & April returned to the lair with a Kraang "portable portal" device. Together, the six used it to enter a Nexus for dimensional travel. They even saw an alternate universe of themselves - the 1987 animated series - while looking for a way home. Instead, they were attacked by Kraang and separated: Leo with Mikey & Raph, then Don with Casey & April. Leo and his two brothers escaped through a portal back to NYC, but were attacked by Tiger Claw and Karai. Soundly defeated, Tiger Claw threatened to kill Mikey if Leo didn't summon Splinter. So, he did. Splinter battled Tiger Claw while the three brothers were tied up on the roof, but Karai used a blowgun to knock Splinter out when he almost defeated Tiger Claw. As Karai moved to attack a helpless Splinter, Leonardo told her that Splinter - Hamato Yoshi - was her true father, but Karai understandably suspected Leo would say anything to save Splinter right then. Barely awake, Splinter used three shurikens to break the three turtles' rope bonds and told them to escape, which they did, but Tiger Claw and Karai still took Splinter to Shredder.
The three turtles took some time back at the lair to bandage their wounds and recover some more weapons, then Leonardo took point in a plan to rescue Splinter. He went in alone and was held by Tiger Claw as Splinter - still affected by the poison dart - was made to fight against Shredder for his life. Another localized earthquake interrupted the fight, and Michelangelo and Donatello used fireworks as a diversion to rescue Splinter with Leo. They took Splinter to a nearby rooftop where he used meditation to work through the poison, but Tiger Claw, Rahzar, Fishface, and Karai found them. In the fight, Tiger Claw broke one of Leo's swords, but he was able to draw his Tanto and catch Tiger Claw off guard. When Tiger Claw countered, Splinter rejoined his sons in the skirmish, Leo only using his Tanto and a rock the whole time. Tiger Claw was gobbled up by the Krathatragon April & Casey were riding, though he eventually escaped after it was pulled back through a portal. They thought Karai fell of the building, but she hid and waited for the end of the battle. Leo even spotted her, but didn't engage.
Mid-combat, April and Casey Jones came riding out of the street riding a Krathatragon (Giant Worm from Dimension X). The worms had caused the mini-quakes every time they struggled against the Kraang's chains. The other trio had escaped the Kraang and shut down the portal the Kraang used to bring the worms into the old pneumatic tube line under NYC, where they'd been milking the Krathatragon for Mutagen. After the fight, under no pressure, Splinter and the turtles continued to refer to Karai as Splinter's daughter, making her reconsider that they were telling the truth.
Another mutation victim appeared, including "Sir Malachi" who introduced the turtles to a D&D-like board game called Mazes & Mutants, then waited for them to discover LARP-ing (Live Action Role Playing) and create an illusion of their game coming to life. Leonardo had been the Game Master for the board game, but a Paladin for the LARP. Baxter Stockman was turned into a fly hybrid for failing the Shredder, and overheard the turtles trying to give Donatello's newly-created Retro-Mutagen to Kirby O'Neil (aka Wingnut). They broke the vial of Retro-Mutagen in the fight, so Baxter kidnapped April as a hostage in exchange for more Retro-Mutagen. Leonardo and Donatello went with Casey to rescue April, and discovered April was immune to mutagen in the process. The four reunited with Raphael and Michelangelo, who'd managed to track down Wingnut, but Baxter stole the Mutagen back. A game of keepaway ensued, but eventually Kirby was successfully changed back. Afterwards, Splinter explained to his sons that he wasn't upset about Donatello's second dose of Retro-Mutagen going to Kirby, or that it could take months to make another batch, because his place wasn't in the human world anymore, but with them, so he wouldn't be seeking to use the Retro-Mutagen for himself.
Slash reappeared teamed up with Newtralizer, powering teleportation bracelets with plutonium. The duo was technically helping the turtles out by taking out the Kraang, but Newtralizer didn't care if humans were hurt along the way, while Slash did. The turtles were at the docks when the Kraang brought a Walker through one of their portals, when Newtralizer hijacked the Walker and turned on Slash. After Raph saved Slash from getting stomped on, he decided to ally with the turtles in the fight. Casey Jones showed up to help out and together they defeated the Newtralizer and his hijacked Walker. Michelangelo defeated a mutant pizza that turned his brothers into Pizza Face-zombies, and Tiger Claw returned with a plan to use Karai to locate the turtles' lair. She tricked Leonardo into thinking she believed she was Hamato Miwa, and Splinter suspected it, but let her discover the truth. Leo was upset about being deceived, but Karai agreed to lead Tiger Claw away with the four turtles protecting her, Raphael the most reluctant after her deceit. In the fight, Karai was recaptured by Tiger Claw and returned to Shredder as a hostage.
After Mikey recovered, Leonardo wanted to rescue Karai, but his brothers were reluctant. "So I'm only the leader until I tell you to do something you don't want to?" On their way to rescue her, they literally ran into Anton Zeck, a thief who had been using invisibility at the time. Zeck had stolen Shredder's helmet - the Kuro Kabuto - for Ivan Steranko, a dealer in relics. Leonardo took the helmet to Shredder to trade it for Karai, and his brothers followed suit, but they accidentally recovered a robot-shaped Karai instead of the real one.
Operating independently from Shredder, the Kraang tried to enact Plan 10: "The switching of Superior Kraang Minds with Inferior Human Minds." In the process, Raphael's mind got switched with a Kraang's, but one big benefit was Raph getting a glimpse of the Kraang's invasion plan. They needed every ally they could get, and went to rescue Karai again against Splinter's advice. Leonardo's plan actually worked in the "rescue Karai" aspect, but after Karai was safe in the lair, she still asked what happened in the past. After Splinter told her how Tang Shen died, she wanted vengeance on the Shredder. She sneaked out and Leonardo tried to help her, but she knocked him out so he wouldn't follow her. Instead, Splinter and the turtles went to rescue her, but Shredder held Karai captive over a vat of mutagen. Shredder knocked Karai's cage into the Mutagen, transforming her into a snake hybrid that could also slip back into a human form.
One last diversion involved an evil spirit - Ho Chan - being let out of an ancient dagger, which eventually possessed Leonardo, Raphael, and Michelangelo so they would help him gain a corporeal form again. In the fight, Ho Chan could tell April had powers, and revealed that her friend Irma had some kind of power as well. This was foreshadowing of the fact that the hitherto minor character Irma, seen as a background friend from April's normal human life, was actually a Kraangdroid in disguise that was spying on April. A spymaster of disguise, mimicry, and an expert on human society, "Irma" was actually Kraang Sub-Prime all along, though his identity wasn't revealed until the final episode of Season 2.
Leatherhead contacted the Turtles to alert them to the Kraang's invasion beginning, but his message didn't reach the Kraang communication orb in Donnie's lair until Michelangelo knocked the "portable portal" device into activating again. Then, Michelangelo got desperate to help his friend and smashed the orb until it stopped working entirely. His brothers were furious at his many screw-ups in a span of minutes, so as Leonardo formulated a plan, part one was "Mikey stays here." Mikey did not stay, and jumped into the portal to Dimension X ahead of his brothers, so after only a minute or so they followed. Because time in Dimension X ran faster proportionally to that of Earth (Chronicles of Narnia style), Mikey was actually in Dimension X for several months. As a result, he learned how to survive in Dimension X, earning Raphael and Donatello's respect almost immediately when Mikey saved them from several Dimension X monsters in a row. That part Leonardo thought was pretty cool, seeing his little brother so capable and in his element. However, when Mikey started acting like the de facto leader, Leonardo was much more put out, having worked so hard to earn the position back home. Eventually, they found Leatherhead, but in Dimension X "many decades" passed for him, aging him significantly but not dampening his spirit. Leatherhead took them to the "Hive Factory" where they could attempt to destroy the Kraang's ability to produce more Kraangdroids. They made a major dent, but it was Mikey who thought to grab a piece of a Kraang "power cell tree" - blowing the Hive to bits and also securing a power source for the Turtle Mech Donatello was developing. Humbled by Mikey's ingenuity, Leonardo made sure to praise his brother for his quick thinking - which wasn't in Dimension X where "crazy backwards dude [Michelangelo] is King," but on Earth. With the time differential, Donatello calculated the Kraang invasion would only be set back several hours, a day at the most, so they had to prepare.
Shredder and Kraang Prime made a formal alliance and the Invasion officially began, the Season Finale of Season Two. FootBots chased Irma and April until April made the decision to bring Irma to the lair for safety. Donatello was finishing preparations on his Turtle Mech while Raphael and Casey were scouting, but Leonardo insisted they establish a secondary base outside of the city because the Turtle Mech wasn't ready yet. Donnie and Leo butted heads over the issue until Irma and April showed up at the lair. Splinter and the three turtles balked at April's decision to bring a stranger, which proved a fatal mistake as Kraang Sub Prime revealed himself from within Irma's robot body. A fight broke out in the lair, and Kraang Sub Prime used several portals to bring in reinforcements. The Kraang began their attack at the same time they were attacking the lair so the turtles would be occupied. The Kraang destroyed the lair and put the turtles on the run through the sewers while Raph and Casey were still out as Splinter held off the Kraang. At a T-intersection, the three turtles and April had a choice to head towards the Turtle Mech or towards the city to find Raph & Casey. Leo and Donnie fought again, but the Kraang found them, so Leonardo ordered Michelangelo and Donatello to take April and find Raph & Casey. Leonardo ran off as a decoy and overheard the Kraang talking about capturing the turtles for Shredder, but it was a trap to lure Leonardo away from his brothers and straight into Shredder's hands. FootBots kept attacking Leonardo in waves until he was nearly exhausted and down to his Tanto again, then Shredder's mutants attacked him too - Tiger Claw, Fishface, and Rahzar. He fended the three of them off with only hand to hand combat, but Shredder dealt the blow that knocked him unconscious.
Tiger Claw and the other mutants used Leo's phone to find out that the turtles were waiting for him at April's Dad's apartment. So, naturally they threw the unconscious Leonardo through the nearest window. Leo was barely breathing, plastron coming loose, shell cracked, right leg and left shoulder hurt, and still unconscious. Raphael was able to carry him to their escape vehicle - Mr. O'Neil's old "hippie van" Volkswagon Type 2 - but later Casey Jones used the same van in the middle of a fight, jumping it on a ramp straight into the giant-sized Kraang Prime. After this - while in his worst physical condition of his life - is when Leonardo is pulled into Ariel.
-SEASON THREE- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_3%29
I'm just linking this one because this is beyond Leonardo's pull point, but it shows that he can and does recover from his injuries eventually. Most notably, his throat was damaged during the fight, explaining the drop in pitch, and he was left with a limp on his right side and a hurt shoulder on his left. He remarks to Raphael after waking up that he doesn't think he'll ever be the same again, and it takes a Mutant attack to shake him out of his slump.
Roughly 16 years before "present" (2012-ish), a much more human conflict came to a head. Hamato Yoshi and Oroku Saki were raised together, although Oroku Saki had been stolen from the Foot Clan as a baby. While the two had always been brotherly rivals, their mutual affection for a girl named Tang Shen tore them apart. In Saki's eyes, Yoshi stole Tang Shen from him. Angry words were said and the two men parted ways no longer friends. Hamato Yoshi and Tang Shen were married, and a daughter came into their lives: Miwa. But Saki chose to have vengeance over friendship, and he returned to burn Yoshi's life to the ground. In the chaos, Saki attacked Yoshi personally, and a blow that was meant for Yoshi struck Tang Shen. Once again, Saki blamed Yoshi for stealing Tang Shen from him, and so he stole Miwa - away from Yoshi's eyes, so that he believed her to be dead, just like Tang Shen.
During Yoshi's bereavement, he made the decision to move to New York City. One day, after he went to the pet store and picked up four baby turtles, the two strings of fate became tangled. Hamato Yoshi happened to walk a Kraangdroid, and the man seemed unusual, so he followed the man into an alleyway where TWO of the same man - as all Kraangdroids are manufactured the same way - were conversing while holding a canister of Mutagen. Having been discovered, the Kraangdroids attacked along with two of their nearby fellows, and Yoshi defended himself. He knocked the Mutagen out of their hands and won the fight, but because the Mutagen was spilled and he dropped the glass bowl holding the turtles, the five of them were all changed. Hamato Yoshi became more animalistic, morphing into an anthropomorphic rat and began calling himself "Splinter" instead. The four turtles became more human, and Splinter chose to adopt them as his sons, calling them "the unlikeliest of families" - but a family nonetheless. He named the four turtles after his favorite painters and sculptors from the Renaissance: Leonardo, Raphael, Donatello, and Michelangelo.
During the next 15 years, the four turtles never went above the surface. Splinter helped them acquire some human paraphernalia along the way to furnish their lair with, and weapons to train with, etc., but for Leonardo in particular nothing impacted him as much as discovering the television show Space Heroes - an animated parody of Star Trek: The Animated Series. The character of Captain Ryan - aka Captain Kirk - became a role model for Leonardo, and he aspired to be as great a hero before he became the formal leader of the turtles. Leonardo learned a lot of scattered Japanese phrases and form names in that time, as well as calligraphy. He took Splinter's teachings to heart, not just his fighting techniques, and is officially the oldest of the four, being the Big Brother to all three of the other turtles. Michelangelo became the family cook and they survived mostly on worms & algae all those years, training in ninjutsu day in and day out - unless they were skating together through the sewers or playing each other on their arcade games in the lair.
-SEASON ONE- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_1%29
On their 15th Mutation Day, Leonardo asked for what the other three turtles must have discussed at length beforehand: to go up on the surface and explore. Reluctantly, Splinter agreed, and they discovered - among other things - the almighty pizza. Oh and April O'Neil getting kidnapped by the Kraang. Of course, the turtles didn't know it was the Kraangdroids, they just tried to fight them off and lost because they couldn't fight as a team. Trying to regroup, Splinter agreed they needed a leader and Leonardo asked for the position. So granted, Leonardo decided they need to stake out a building in hopes of finding April's kidnappers, which worked after a fashion. In the struggle, another canister of Mutagen rolled out of the van used to take her away. The lone human kidnapper was Snake, who told them the group was called "The Kraang". Unfortunately, Mikey let Snake escape; fortunately, Leonardo and Raphael silently agreed to discuss their plan in front of a hiding Snake so that they'd prepare for the wrong kind of attack. Back at the lair, Leonardo solidified their true plan with a pep talk from Splinter while Donatello made them climbing gear. They snuck into the Kraang's satellite facility and and discovered the Kraang's identity as aliens in robot bodies. They rescued April and defeated a mutated Snake (plant hybrid now called Snakeweed by Mikey), but a small force of Kraang escaped with April's father. The four turtles dropped April off at her aunt's place and promised to help her reunite with her father, then returned to the lair. Leonardo found out that the reason Splinter made him leader was because he asked to be, and that choices wouldn't always be right or wrong. Leo had to realize he wouldn't be a leader immediately, but learn how to become a good one. A news report on the incident - "Ninjas in New York" - reached Oroku Saki all the way in Japan, where he recognized the Hamato crest on a recover shuriken. Oroku Saki had become Shredder, the leader of the Foot Clan he was a part of by birth, and decided to fly to New York to destroy his old nemesis. Thus the world-threat of the Kraang intersected with the personal vendetta of the Shredder, even if the turtles didn't know it yet.
Each of the turtles had their own personal flaws to work on and the next several episodes were devoted to that. Raphael's temper almost got the turtles exposed to the whole world, and then Michelangelo's good faith in people enabled him to befriend Shredder's star pupil, Chris Bradford. The turtles successfully thwarted Bradford and his Foot ally, Xever, using teamwork and identifying the need to switch opponents mid-combat, but Splinter warned the boys that the fight was only beginning. For Leonardo, his problem was that he didn't command enough respect to just issue orders his brothers would follow. By trying to stick with brothers as family, they got into more trouble and created an enemy for themselves in Baxter Stockman, which escalated with the help of some tech Donatello created and Baxter acquired thanks to Mikey's negligence. They finally came clean with Splinter, regrouped, and defeated Baxter, but Leonardo would need a lot more experience before his brothers would respect him. Likewise, he had to understand that being a Leader would mean making unpopular decisions. Splinter advised that they look deeper into their ninja training for the secret to fighting someone in armor, and Leonardo took that lesson to heart as well. While fighting the Kraang, Donatello became disheartened about his ability to fight with his bo staff, and successfully created a robot drone called Metalhead that Donatello could control with a video-game remote. April discovered a Kraang plot to pollute the water supply of NYC, so Donatello used Metalhead during the ensuing fight. Unfortunately, since Metalhead was created from Kraang tech, a Kraang was able to take it back over, and Donatello had to defeat his own drone after joining his brothers in person. For as intelligent as Donatello is, he was struggling with everyday wisdom.
The turtles had to fight a mind-reading ally of the Kraang called Doctor Falco, and during that time Shredder descended upon NYC. He put Xever in charge, bringing Xever's allies the Purple Dragons into the fight. The turtles discovered them roughing up a blind restaurant owner, Mr. Murakami, and Leonardo showed the leader Fong mercy. Raphael gave Leo a really hard time about it, but later on Murakami got kidnapped by Xever and the Purple Dragons. When the turtles were about to be defeated by Xever and Bradford, Fong returned Leonardo's sword to him, and they managed to escape. Leo learned that mercy wasn't a weakness, and Splinter's other lesson about seeking victory not fairness was also highly relevant. The Kraang and Shredder's plots converged accidentally when they got a chance to rescue April's father, but the effort only resulted in discovering the Kraang were planning to detonate a mutagen bomb over the city. Xever and Bradford attacked the turtles while Donatello was trying to diffuse the bomb. Donatello was successful, but rather than fail the Shredder again, Bradford tried to unleash the mutagen on the six combatants so they'd all perish together. Instead, Xever was turned into a barracuda hybrid called Fishface and Bradford himself became a dog hybrid mutant called Dogpound. Shredder himself attacked the turtles and they barely escaped with their lives, which shot their confidence down immensely and made Splinter panic for fear of losing his second family. He made the turtles train hard for weeks before permitting them to surface again.
What finally brought them up again was a plot from Shredder to destroy their lair in the sewers, even if he didn't know the exact location. The turtles fought the newly mutated Dogpound and lost, furthering their own fear, but April still had enough courage to uncover Shredder's plan. The brothers fought Dogpound again and won, saving the lair, and Splinter apologized for inciting the panic. Like many young people learning powerful skills, Leo and Raph got over-confident in their abilities as compared to Donnie and Mikey, and when the four decided to strike against the Purple Dragons for stealing from April, they split up into "A Team" and "B Team" - very much against Donatello and Michelangelo's wishes. A brotherly spat brought out into the streets got them mixed up in an alliance between Dogpound and Baxter Stockman. Leo and Raph were left outrunning Baxter's Mousers, trying to fend off a relentless robot army to the point of exhaustion. Only once Leo and Raph rejoined with Donnie and Mikey were the two groups able to defeat their individual foes together AND they really shouldn't have instigated the fight in the first place.
The Kraang lost control of a captive alligator mutant who eventually became their ally thanks to Mikey's compassion, and he named him Leatherhead. The brothers took a Kraang power cell into their protection at Leatherhead's request, to keep it safe so the Kraang didn't use it to power their portal to Dimension X. The turtles escaped the Kraang by powering a train car with the power cell, which Donatello turned into the Shellraiser vehicle. Dr. Victor Falco returned as a rat hybrid mutant after a spill in his makeshift lab, and even managed to use his mind-control powers on Splinter himself. Together, the four turtles had to defeat their father (who wasn't holding back now like in their training sessions) without seriously injuring him. Leonardo used Splinter's picture of himself as Hamato Yoshi with his wife and daughter to remind him who he was, and called out to him as father, which brought Splinter out of The Rat King's control so Splinter could deal the finishing blow.
Raphael had gotten on Leonardo's case before about his chosen methods for leading the brothers during battle, but not as rough as when Snakeweed reappeared and kidnapped someone. Leo snapped and told Raph he could lead since he thought he could do it better, and when Leo went to blow off some steam, the Foot Clan attacked. That was when Karai found him, a female ninja better than the nameless Foot warriors. She toyed with him and let him go, leaving him to rest back at the lair while his brothers went out on a mission. Splinter found out that Leo shucked his responsibility, with Leo whining that his brothers didn't understand the pressure he was under, and that they didn't appreciate him. Splinter told his son "it doesn't matter if the burden is heavy, only that you carry it." Of course, it didn't sink in right away. Leo was tasked with catching up to the other turtles, but Karai waylaid him. She told him to meet her at the Byerly building at midnight, so Leonardo went to April for advice, who promptly scolded him - physically and verbally - for hanging out with a member of the Foot Clan. Leo insisted she was different, but April wasn't convinced, and asked only that he be careful. Just to be safe, she told Donatello where Leo was heading. Meanwhile, the trio of brothers wasn't faring so well, with Raph freezing up at trying to make decisions that would risk his brothers' lives fighting Snakeweed. Donnie helped Raph get Mikey home safe - but Leo wasn't there or with them, a fact Splinter noticed immediately. While Raphael now understood Leonardo's position, they still had to find him. Thanks to Donatello's text from April, Raphael knew where to find Leo, but Raph also caught him in the middle of talking to Karai. Karai was trying to convince Leo to steal the sword of Miyamoto Musashi, but Leo refused, so Karai pinned Leo to the top of the building - only Leo didn't sound too upset about it when Raph found them. Snakeweed tracked Raphael down and with indirect help from Karai, the two brothers defeated Snakeweed after a rare verbal apology from Raphael. Leo had to tease him about that a bit, but ultimately they reconciled, and Leo kept right on crushing on Karai too.
That's why Raphael kept close tabs on Leonardo when he started showing off during a fight. He kept trying to convince Leo otherwise, but Leonardo wouldn't give up thinking Karai had a good side to her. He waited for her alone on a rooftop, and the fought again until she ran off again. Leo warned her that "if you come after them, I'll come after you." An improved Kraangdroid sent by one of the Kraang's shell organization "The Worldwide Genome Project" attacked April and the turtles tracked it down after rescuing her, but Karai followed them. Donatello and Mikey found out the backstory mid-combat, right before Karai jumbled a bunch of DNA into a giant Mutagen canister and created a monster, then just left the fight. Leonardo felt betrayed initially, but ultimately took responsibility for allowing Karai to get involved - and for being blinded by his attraction to her. He came clean to his family and to April, and insisted he'd give up liking her, but such things are easier said than done. Leonardo's mistake also helped Karai bring a piece of Kraang technology to the Shredder's doorstep, which would prove costly as it ultimately led to Shredder allying himself with the Kraang. The next of Shredder's alliances the turtles discovered was with Baxter Stockman, which was how Xever's Fishface form became land-compatible again.
Since the turtles were using the Kraang's power cell for their Shellraiser vehicle, it was only a matter of time before Donnie's defensive mechanisms on it failed. The Kraang got it back and when they couldn't retrieve it, they confessed to Leatherhead about losing it. Eventually, Leatherhead calmed down enough to tell them the repercussions of the Transporter being operational - that the Kraang could bring things from Dimension X again, namely backup forces. He remembered and drew a honeycomb-like symbol for them to help them find the building, which they eventually figured out was for TCRI - another shell organization like the WWGP. With April and Leatherhead's help, they sneaked into the TCRI building and even got all the way to the top floors, but the Kraang had filled the upper floors with noxious atmosphere from Dimension X and the turtles passed out from lack of oxygen. When they woke up, they were captured, and had to fend off the Kraang while holding their breaths. Leatherhead sacrificed himself to try shutting down the portal from the other side, leaving the turtles to escape the building and unfortunately with the portal intact. However, they did find out one of the Kraang's ultimate objectives: April, not her father. Donatello tried to help them spy on the Kraang with a cockroach, but the roach ended up mutating during its mission, leaving the turtles to both stop the Kraang's plot to drill through the Earth's crust AND stop the mutant roach at the same time. It didn't help that Raphael has a roach phobia, which he confronted but didn't get over during the fight with Donatello's roach.
Both Shredder's forces and the turtles went after the Kraang's newest weapon - the Spacial Endal Particle Disruptor - and ended up disrupting each others' efforts. Baxter took the fall for the blunder so that he could try to get the turtles plus Dogpound and Fishface all in the same gambit, but the turtles managed to make a temporary truce with Shredder's henchmen and survive Baxter's maze of lethal traps. Karai tried to get the same chance, but understandably Leo's three brothers were incredibly resistant to the idea. Leonardo believed her and Karai suggested they steal one of several missile launchers from a shipment that Shredder was receiving. To test her, they made her get it herself, but ended up doubling back on the promise to team up against the Kraang for the opportunity to take down Shredder. In the ensuing threeway battle with Shredder and a Kraang scout ship, Karai told Leonardo Shredder was her father, and the fight ended in a standstill between the Foot Clan and the turtles. Leonardo did manage to shoot down the Kraang ship with the missile launcher, but still felt bad for losing their chance to have Karai as an ally. In fact, Karai took the next opportunity to target April specifically while the guys took a mini-sub Donnie made to the bottom of the East River, trying to destroy another remote Kraang facility that was polluting the water supply with Dimension X water. After that, Splinter suggested - and Leo agreed - that with both Shredder's forces and the Kraang after April, she should live with them in the sewers for awhile.
In desperation to have a stronger army, Shredder contracted with the Kraang to create an army. Their first plot was to mutate existing human Foot Ninjas, which led to their incompetent human ally The Pulverizer (Timothy) becoming a mole despite Donatello's hesitation. At the same time, Splinter insisted the turtles learn different fighting styles. Leonardo ended up with Donatello and Mikey got Leo's swords. They didn't last one fight before Leo suggested they switch back - one of the few times Leo went against Splinter's lesson, thinking it was to help them all stay alive. Splinter wasn't amused and took their weapons away instead to teach them resourcefulness. During the fight, Timothy insisted on trying to become a mutant to be more awesome, but only succeeded in turning into a blob. The defeat solidifed an alliance between the Kraang and Shredder, leading to the development of FootBots - robot ninjas with Foot Clan training, but bodies made similar to the Kraangdroids. Another experiment in the FootBot development was on a wasp that stung Leonardo, turning him into a drone protector for the mutant's eggs that could infect others zombie/werewolf-style. He succumbed and turned his brothers while defending the egg, but Michelangelo saved them by completing an antidote Donatello developed.
Donatello decrypted a secret message from April's father, but it was a Kraang trap to get the turtles to take Kirby O'Neil back with them so he could find April. In actuality, Kirby was being mind-controlled by the Kraang so that he'd turn April over to the Kraang. While Donatello managed to break Kirby out, they also unleashed a Kraang captive criminal dubbed Newtralizer. They defeated the Newtralizer while April found a Kraang communication orb, which helped alert the turtles that the Kraang were planning to start their invasion by bringing in a tank-like fortress called the Technodrone from Dimension X.
Splinter advised Leonardo that there may be a need for sacrifices in the upcoming battle, with the fate of the world at hand. With the turtles away, Mind-Controlled Kirby managed to lead April away from the lair and into Karai's hands. April was used as bait for Splinter to fight Shredder while the turtles attacked TCRI with their full strength, the primary goal being to knock out the portal before the Technodrone could come through. Metalhead was sent in first while the turtles descended on the upper levels of TCRI on gliders. The Kraang's SEPD gun might have destroyed the portal, but it had a forcefield around it. Splinter fought Shredder and nearly defeated him, except Karai interfered and Splinter was disheartened to learn she was his daughter Miwa - alive, but raised by Shredder. The Kraang managed to bring the Technodrone to NYC despite the turtle's best efforts, namely involving Leonardo jumping out of the building at the end of a failed blow-it-all-up gambit. Raphael was the one to save him from splattering on the streets. The turtles regrouped back at the lair thinking they could get Splinter's and April's help, but they had to get Kirby un-mind-controlled first. Kirby then explained April would be in the Technodrone by now, so the turtles plotted to sneak in. They succeeded but Kraang Prime came after them so as not to lose the precious Uniquely Attuned Mental Energy that the Kraang had been engineering for so long. Leonardo was able to hold Kraang Prime back long enough to send the Technodrone crashing into the water, but ordered his brothers to take April and escape without him. He dove out at the last second, but scared his brothers long enough they thought he'd died. They celebrated their victory, thinking Shredder and the Kraang were defeated, but it was short-lived.
-SEASON TWO- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_2%29
The turtles still had the Kraang communication orb, and realized that the Kraang were regrouping. They went after a Kraang stealth ship that was delivering mutagen to the Shredder, but ended up dumping canisters all over the city. Among the people affected by the rain of mutagen canisters was Kirby O'Neil and when the boys tried to take responsibility for the accident, April shunned them. The rest of the season primarily used Donatello's tracking devices to locate the canisters and the beings affected by them. First up were mutant squirrels that doubled inside of a person's gut.
As the hunt wore his brothers down, Leonardo suggested they take a break for a training session. Leo had to defend a gate against each of his brothers in turn, but they used their own styles of fighting to get past him. Leonardo took it as an insult, but Splinter advised him that a leader didn't always have to impose their will on their followers. While that was true, the other side to the advice was helping his followers flourish - and thereby earning their respect. Because the brothers didn't listen to Leonardo's orders and wouldn't retreat when he told them to, they were ambushed by the new FootBots in their first fight against them. When Mikey got in trouble, Leo leaped down to save him, but was captured in the process. Raphael, Donatello, and Michelangelo went to rescue Leonardo while Karai insisted this was her vengeance for Splinter taking her mother away. Leo denied that Splinter would do such a thing, but Leo was just bait for the other turtles, and eventually for Splinter himself. However, the four brothers escaped, and Leonardo ended up coming around to the idea of being unpredictable - and slightly unconventional - as a valid fighting technique. Leo defeated Karai and told her that her grudge was misplaced, then they escaped with a smokebomb. Back at the lair, Raphael even apologized, but Leo had to ask Splinter about what Karai accused Splinter of doing. That was when Splinter told Leonardo - and him alone - that Karai was in fact his daughter. Leonardo kept his father's secret for him and didn't tell his brothers.
Later, Timothy tried to fix his mutated state by drinking more mutagen, only to become Mutagen Man, but the turtles froze him in order to stop him, much to Donatello's regret. Next, Mikey nearly exploded from over-exposure on his skin for starters. Two things happened at that time, Dogpound mutated a second time into Rahzar and, after the turtles escaped, Donatello started to develop some anti-mutagen serum in order to reverse Mikey's "Shellacne" condition. Unfortunately, April needed some time to forgive the turtles for the accident not being their fault. Karai tried to commission a special Kraangdroid to kidnap April, but they turned on her and tried to capture April for themselves. It reunited April with the turtles, but it also introduced Casey Jones to the picture as he helped defend April from the FootBots Karai sent after her.
Another victim of the mutagen this season was Raphael's pet snapping turtle, Spike, who transformed into a mutant turtle himself and started going by "Slash." At first, Raphael was delighted to have a new brother, until Slash decided that the best way to free Raphael from the chains holding him back (from becoming a 24/7 crime-fighter) was to eliminate the brothers he professed to hate so much. Leonardo went on a stealth mission alone to recover a mutagen canister, not realizing that Slash had beaten Donatello and Michelangelo within an inch of their lives. While Raphael fended Slash off, Leonardo ended up having a tea party with a little girl (seriously) until the two raging turtles came crashing through her wall. Together, Raphael and Leonardo managed to fend him off until he went over the edge of a building. It didn't kill Slash, but it did send him running and encouraged Raphael to cherish his brothers a little more.
It was after Slash's attack that Raphael discovered Casey going vigilante as well, but too extreme even for Raphael. As a result of one of Raph's tantrums, Casey was able to track him back to their lair, and FootBots were able to track Casey. They barely managed to destroy all of the FootBots before they could report on the lair location. Raphael and Casey had to work together to take down a runner, coming to a mutual understanding in the process.
Soon enough, the turtles learned how deep the Kraang's plot ran - centuries old and very clearly engineering human DNA to create April's specific strain. Thanks to a journalist called Kurtzman, they also realized that the Kraang had already rebuilt TCRI. They wanted to sneak in without April and wipe out the records the Kraang had of April's DNA in order to keep her safe, but April joined them anyway. April was able to overhear Kraang Prime talking to her subordinates, leading to her capture within the TCRI building. Raphael rescued her while Leonardo, Donatello, and Michelangelo fought off April Clones, including a disfigured one that was very strong. Just when April was about to be hurt by the Kraang's devices, she let out a sonic scream-like attack. Back in Donnie's lab, they discovered why - the "specific string of DNA" April has is that of a half-human half-alien mutant. April of course took it harder than the guys did, but it solidified their family unit bond with her and goal to keep her safe from the Kraang.
Leonardo started having recurring nightmares where he failed his brothers and they were dragged off into darkness. A mutant fungus attack made him confront them as their spores caused fear-based hallucinations. For Leonardo, his hallucination also included his brothers saying how he'd let them down. He meditated mid-combat long enough to remind himself he faced his fear every day, and exposed the fungus to sunlight, thus destroying it.
Donnie managed to rewire Metalhead with an AI, but his first mission with them became his last too. The turtles discovered the Kraang capturing Mutants in order to control them the way they did Kirby O'Neil at the end of Season 1. Metalhead managed to open the portal again, but could only keep it open manually. To get the turtles home again through the same portal, Metalhead had to stay behind and hold the portal open. Metalhead self-destructed, but his head blew up through the portal for Donatello to recover. The Rat King tried to make a combat but was thwarted, during which time Shredder returned from a trip to Asia with a new ally - Tiger Claw, a mutant assassin from Asia.
Since Splinter told Leonardo that Karai was his daughter Miwa, Leonardo tried to tell Karai as well, but failed because a localized earthquake interrupted the fight. Leonardo at least convinced Splinter to tell his brothers about their "sister." While they processed that information, Casey & April returned to the lair with a Kraang "portable portal" device. Together, the six used it to enter a Nexus for dimensional travel. They even saw an alternate universe of themselves - the 1987 animated series - while looking for a way home. Instead, they were attacked by Kraang and separated: Leo with Mikey & Raph, then Don with Casey & April. Leo and his two brothers escaped through a portal back to NYC, but were attacked by Tiger Claw and Karai. Soundly defeated, Tiger Claw threatened to kill Mikey if Leo didn't summon Splinter. So, he did. Splinter battled Tiger Claw while the three brothers were tied up on the roof, but Karai used a blowgun to knock Splinter out when he almost defeated Tiger Claw. As Karai moved to attack a helpless Splinter, Leonardo told her that Splinter - Hamato Yoshi - was her true father, but Karai understandably suspected Leo would say anything to save Splinter right then. Barely awake, Splinter used three shurikens to break the three turtles' rope bonds and told them to escape, which they did, but Tiger Claw and Karai still took Splinter to Shredder.
The three turtles took some time back at the lair to bandage their wounds and recover some more weapons, then Leonardo took point in a plan to rescue Splinter. He went in alone and was held by Tiger Claw as Splinter - still affected by the poison dart - was made to fight against Shredder for his life. Another localized earthquake interrupted the fight, and Michelangelo and Donatello used fireworks as a diversion to rescue Splinter with Leo. They took Splinter to a nearby rooftop where he used meditation to work through the poison, but Tiger Claw, Rahzar, Fishface, and Karai found them. In the fight, Tiger Claw broke one of Leo's swords, but he was able to draw his Tanto and catch Tiger Claw off guard. When Tiger Claw countered, Splinter rejoined his sons in the skirmish, Leo only using his Tanto and a rock the whole time. Tiger Claw was gobbled up by the Krathatragon April & Casey were riding, though he eventually escaped after it was pulled back through a portal. They thought Karai fell of the building, but she hid and waited for the end of the battle. Leo even spotted her, but didn't engage.
Mid-combat, April and Casey Jones came riding out of the street riding a Krathatragon (Giant Worm from Dimension X). The worms had caused the mini-quakes every time they struggled against the Kraang's chains. The other trio had escaped the Kraang and shut down the portal the Kraang used to bring the worms into the old pneumatic tube line under NYC, where they'd been milking the Krathatragon for Mutagen. After the fight, under no pressure, Splinter and the turtles continued to refer to Karai as Splinter's daughter, making her reconsider that they were telling the truth.
Another mutation victim appeared, including "Sir Malachi" who introduced the turtles to a D&D-like board game called Mazes & Mutants, then waited for them to discover LARP-ing (Live Action Role Playing) and create an illusion of their game coming to life. Leonardo had been the Game Master for the board game, but a Paladin for the LARP. Baxter Stockman was turned into a fly hybrid for failing the Shredder, and overheard the turtles trying to give Donatello's newly-created Retro-Mutagen to Kirby O'Neil (aka Wingnut). They broke the vial of Retro-Mutagen in the fight, so Baxter kidnapped April as a hostage in exchange for more Retro-Mutagen. Leonardo and Donatello went with Casey to rescue April, and discovered April was immune to mutagen in the process. The four reunited with Raphael and Michelangelo, who'd managed to track down Wingnut, but Baxter stole the Mutagen back. A game of keepaway ensued, but eventually Kirby was successfully changed back. Afterwards, Splinter explained to his sons that he wasn't upset about Donatello's second dose of Retro-Mutagen going to Kirby, or that it could take months to make another batch, because his place wasn't in the human world anymore, but with them, so he wouldn't be seeking to use the Retro-Mutagen for himself.
Slash reappeared teamed up with Newtralizer, powering teleportation bracelets with plutonium. The duo was technically helping the turtles out by taking out the Kraang, but Newtralizer didn't care if humans were hurt along the way, while Slash did. The turtles were at the docks when the Kraang brought a Walker through one of their portals, when Newtralizer hijacked the Walker and turned on Slash. After Raph saved Slash from getting stomped on, he decided to ally with the turtles in the fight. Casey Jones showed up to help out and together they defeated the Newtralizer and his hijacked Walker. Michelangelo defeated a mutant pizza that turned his brothers into Pizza Face-zombies, and Tiger Claw returned with a plan to use Karai to locate the turtles' lair. She tricked Leonardo into thinking she believed she was Hamato Miwa, and Splinter suspected it, but let her discover the truth. Leo was upset about being deceived, but Karai agreed to lead Tiger Claw away with the four turtles protecting her, Raphael the most reluctant after her deceit. In the fight, Karai was recaptured by Tiger Claw and returned to Shredder as a hostage.
After Mikey recovered, Leonardo wanted to rescue Karai, but his brothers were reluctant. "So I'm only the leader until I tell you to do something you don't want to?" On their way to rescue her, they literally ran into Anton Zeck, a thief who had been using invisibility at the time. Zeck had stolen Shredder's helmet - the Kuro Kabuto - for Ivan Steranko, a dealer in relics. Leonardo took the helmet to Shredder to trade it for Karai, and his brothers followed suit, but they accidentally recovered a robot-shaped Karai instead of the real one.
Operating independently from Shredder, the Kraang tried to enact Plan 10: "The switching of Superior Kraang Minds with Inferior Human Minds." In the process, Raphael's mind got switched with a Kraang's, but one big benefit was Raph getting a glimpse of the Kraang's invasion plan. They needed every ally they could get, and went to rescue Karai again against Splinter's advice. Leonardo's plan actually worked in the "rescue Karai" aspect, but after Karai was safe in the lair, she still asked what happened in the past. After Splinter told her how Tang Shen died, she wanted vengeance on the Shredder. She sneaked out and Leonardo tried to help her, but she knocked him out so he wouldn't follow her. Instead, Splinter and the turtles went to rescue her, but Shredder held Karai captive over a vat of mutagen. Shredder knocked Karai's cage into the Mutagen, transforming her into a snake hybrid that could also slip back into a human form.
One last diversion involved an evil spirit - Ho Chan - being let out of an ancient dagger, which eventually possessed Leonardo, Raphael, and Michelangelo so they would help him gain a corporeal form again. In the fight, Ho Chan could tell April had powers, and revealed that her friend Irma had some kind of power as well. This was foreshadowing of the fact that the hitherto minor character Irma, seen as a background friend from April's normal human life, was actually a Kraangdroid in disguise that was spying on April. A spymaster of disguise, mimicry, and an expert on human society, "Irma" was actually Kraang Sub-Prime all along, though his identity wasn't revealed until the final episode of Season 2.
Leatherhead contacted the Turtles to alert them to the Kraang's invasion beginning, but his message didn't reach the Kraang communication orb in Donnie's lair until Michelangelo knocked the "portable portal" device into activating again. Then, Michelangelo got desperate to help his friend and smashed the orb until it stopped working entirely. His brothers were furious at his many screw-ups in a span of minutes, so as Leonardo formulated a plan, part one was "Mikey stays here." Mikey did not stay, and jumped into the portal to Dimension X ahead of his brothers, so after only a minute or so they followed. Because time in Dimension X ran faster proportionally to that of Earth (Chronicles of Narnia style), Mikey was actually in Dimension X for several months. As a result, he learned how to survive in Dimension X, earning Raphael and Donatello's respect almost immediately when Mikey saved them from several Dimension X monsters in a row. That part Leonardo thought was pretty cool, seeing his little brother so capable and in his element. However, when Mikey started acting like the de facto leader, Leonardo was much more put out, having worked so hard to earn the position back home. Eventually, they found Leatherhead, but in Dimension X "many decades" passed for him, aging him significantly but not dampening his spirit. Leatherhead took them to the "Hive Factory" where they could attempt to destroy the Kraang's ability to produce more Kraangdroids. They made a major dent, but it was Mikey who thought to grab a piece of a Kraang "power cell tree" - blowing the Hive to bits and also securing a power source for the Turtle Mech Donatello was developing. Humbled by Mikey's ingenuity, Leonardo made sure to praise his brother for his quick thinking - which wasn't in Dimension X where "crazy backwards dude [Michelangelo] is King," but on Earth. With the time differential, Donatello calculated the Kraang invasion would only be set back several hours, a day at the most, so they had to prepare.
Shredder and Kraang Prime made a formal alliance and the Invasion officially began, the Season Finale of Season Two. FootBots chased Irma and April until April made the decision to bring Irma to the lair for safety. Donatello was finishing preparations on his Turtle Mech while Raphael and Casey were scouting, but Leonardo insisted they establish a secondary base outside of the city because the Turtle Mech wasn't ready yet. Donnie and Leo butted heads over the issue until Irma and April showed up at the lair. Splinter and the three turtles balked at April's decision to bring a stranger, which proved a fatal mistake as Kraang Sub Prime revealed himself from within Irma's robot body. A fight broke out in the lair, and Kraang Sub Prime used several portals to bring in reinforcements. The Kraang began their attack at the same time they were attacking the lair so the turtles would be occupied. The Kraang destroyed the lair and put the turtles on the run through the sewers while Raph and Casey were still out as Splinter held off the Kraang. At a T-intersection, the three turtles and April had a choice to head towards the Turtle Mech or towards the city to find Raph & Casey. Leo and Donnie fought again, but the Kraang found them, so Leonardo ordered Michelangelo and Donatello to take April and find Raph & Casey. Leonardo ran off as a decoy and overheard the Kraang talking about capturing the turtles for Shredder, but it was a trap to lure Leonardo away from his brothers and straight into Shredder's hands. FootBots kept attacking Leonardo in waves until he was nearly exhausted and down to his Tanto again, then Shredder's mutants attacked him too - Tiger Claw, Fishface, and Rahzar. He fended the three of them off with only hand to hand combat, but Shredder dealt the blow that knocked him unconscious.
Tiger Claw and the other mutants used Leo's phone to find out that the turtles were waiting for him at April's Dad's apartment. So, naturally they threw the unconscious Leonardo through the nearest window. Leo was barely breathing, plastron coming loose, shell cracked, right leg and left shoulder hurt, and still unconscious. Raphael was able to carry him to their escape vehicle - Mr. O'Neil's old "hippie van" Volkswagon Type 2 - but later Casey Jones used the same van in the middle of a fight, jumping it on a ramp straight into the giant-sized Kraang Prime. After this - while in his worst physical condition of his life - is when Leonardo is pulled into Ariel.
-SEASON THREE- http://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_%282012_TV_series%29_%28season_3%29
I'm just linking this one because this is beyond Leonardo's pull point, but it shows that he can and does recover from his injuries eventually. Most notably, his throat was damaged during the fight, explaining the drop in pitch, and he was left with a limp on his right side and a hurt shoulder on his left. He remarks to Raphael after waking up that he doesn't think he'll ever be the same again, and it takes a Mutant attack to shake him out of his slump.
