Wikia

Dr. Baxter Stockman is a usually evil scientist, often allied with Shredder and/or Krang. In each version, he is depicted as the creator of the Mousers, machines meant to seek out and destroy sewer rats (not mice, in spite of their name). Nevertheless, there are several differences among his various appearances. In most incarnations, he is forced into an alternate form (cyborg, fly mutant) that causes his sanity to erode even further.

In the 2003 TMNT series Baxter Stockman started working with the turtles friend "April O'Neil" who suddenly found out that Baxter was making mousers to serve "The Shredder" once she found this out she decided to put a stop to it and so she did. But all this meant Baxter was going to get beaten by the Shredder so he got tortured and eventually ended up on a wheelchair. But in Season 1 the Shredder blew up Aprils shop "2nd Time Around", but Shredder didn't think they survived so he sent Stockman to investigate. Stockman found out the turtle's survived but didn't want to get beaten up by the Shredder so he lied and said the turtles died and got a Utrom exoskeleton as his prize. But once the Shredder found out he chopped Baxter's body off. Later on in Season 2, he reappeared with a body of a spider to stop the turtles from seeing Shredders secret origins. But the Shredder failed to kill the turtles again. So Baxter quit working for the Foot and started working with Leatherhead, a mutant crocodile, but once the Turtle found out that Leatherhead was nice and Stockman was bad they kicked stockman out of there!