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.