When the "Ultimate Drako" attacks the lair, he sends each of the turtles to another world or an alternate universe (Splinter is sent to the Battle Nexus, and Casey is just left in the lair, wondering where everyone has gone).
We see where Donatello was sent in Same As It Never Was. He is sent to a dystopian version of his universe, 30 years in the future. In this universe, the Shredder rules the entire world with an iron fist (literally), and the Ninja Turtles have gone their separate ways.
Leonardo argues with Raphael saying they shouldn't have gone back for Splinter, as it would only have killed them too. By this point, Leo had lost all tolerance towards Raphael, and had left the team. Raphael did likewise. So Michelangelo was left on his own. At some point, Casey died, Raphael lost one eye, and Michelangelo lost his left arm. Leonardo is the only one of the dystopian turtles not to keep his mask, though that may be because he wears sunglasses.
Eventually, after Donatello gets the turtles back together, a heavily scarred Leonardo fights with them in a last ditch attempt to kill the Shredder. Leo battles Karai with a single katana, and beat her. However, just as he was to deliver the finishing blow, a Karai Bot distracted him, causing him to turn and destroy it, allowing Karai to wound him with her sword, killing him. Dystopian Raphael later crawls to the dead Leonardo, fatally wounded himself, calling Leo's name and trying to apologize for the years he spent hating Leonardo.
Leonardo's contributions would help Donatello kill Ch'rell, thus avenging the rebellion.
- Due to constantly wearing sunglasses, it was assumed by many that dystopian Leonardo was blind. However, TMNT4Kids (the 4Kids Entertainment-to-fans liaison) said that the script never mentioned him with any kind of vision impairment, only "scarred".