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When the Ultimate Drako attacked the lair, he sent each of the Ninja Turtles to another world or an alternate universe (Splinter was sent to the Battle Nexus, and Casey is just left in the lair, wondering where everyone has gone).
In Same As It Never Was, it is revealed that Donatello was 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. This took place sometime after the Donatello of this reality disappeared under mysterious circumstances, and Splinter was killed saving his other three sons. Raphael blamed Leonardo for Splinter's sacrifice, believing that they abandoned their sensei. Without Donatello's calming presence, the two parted ways for good. At some point, Casey died, Raphael lost one eye, and Michelangelo lost his left arm.
Donatello called together the estranged brothers once again, and Raphael and Leonardo nearly came to blows over their old argument. Donatello intervened, revealing his presence in this dimension, and Raphael was delighted to see him.
During the battle against the Shredder that ensued, Leonardo was stabbed to death by Karai. The enraged Raphael attacked her to avenge his fallen brother, but was also mortally wounded by Karai. In his final moments, he crawled to Leonardo, calling his name, trying to apologize for all the years he spend resenting his eldest brother.
Raphael was the last of the dystopian Turtles to be killed (first Michelangelo, then Leonardo, then Raphael). It was eventually the other-dimensional Donatello that killed the dystopian Shredder, avenging the deaths of his alternate-dimension brothers, and leaving a middle-aged April to help rebuild the world.