Later on, the episode "Head of State" revealed the reasons behind Bishop's change of heart. Roughly fifty years prior to 2105, he and Baxter Stockman, both still working for the E.P.F., finally realized Bishop's ambition of a super-soldier army in the form of what Stockman named "Organic Mousers": biped one eyed dinosaur like creatures able to withstand heavy damage and controlled by sound. A lab accident seemingly killed Stockman; Bishop himself would have died if not for the actions of one of the E.P.F.'s alien test subjects, who saved his life though due to its inhumane treatment, Bishop didn't expect him to.
Surprised and touched that an alien which had been imprisoned and experimented upon by the E.P.F. still had enough mercy in it to save him, Bishop's viewpoint on aliens changed radically, and he began to work for far more peaceful solutions, and turned his efforts into befriending them instead, leading to the creation of the Pan-Galactic Alliance. It was this change of heart that saved him when he was kidnapped by the still-living Baxter Stockman, who, seething at Bishop's abandonment fifty years ago and still incapable of building himself a new body, wished to take Bishop's body as his own; but convinced by Leonardo that the world Bishop helped create was one where even he could live a normal life, he abandons his plan. Immediately afterward, as the abandoned E.P.F. base where Stockman had taken Bishop was destroyed by Stockman's organic mousers, Stockman was once again placed in mortal peril. This time, however, Bishop did not hesitate and managed to save his friend's life.
With both Bishop and Baxter safe, Bishop informs Doctor Stockman that with the advancement in human technology over the last 100 years creating a new body for Stockman is easy. He also tells him that the Department of Agriculture expressed interest in his mousers and he wanted him to meet them, which the latter accepted.
Finally, Bishop appeared in the episode "The Day of Awakening", where he informed the Turtles about Sh'Okanabo's takeover of the lunar settlement Moonbase Bishop, recruited them in his attempt to stop the alien, and provided them with the weaponry that eventually killed him.