In the year 2105, Baxter Stockman was still alive after 100 years, mixing his brain with alien DNA. This allowed his brain to no longer require any external life support systems, and could now move on its own with green tentacles attached to it. He sent creatures called Organic Mousers (which he created, while still under Bishop's employment off and on in the Earth Protection Force, to fight off aliens) after Bishop because he felt he was betrayed years ago, when Stockman was left behind by Bishop when a failed experiment accidentally triggered a bio-chemical reaction, which caused the Earth Protection Force laboratory to collapse. Bishop was actually trying to save Baxter when he became trapped under rubble, and one of his alien captives saved him. Still incapable of building himself a new body, Stockman wished to take President Bishop's body as his own. However, he almost kills Bishop by renovating his head with the help of his brain transplanting device, but is convinced by Leonardo that the world that the president helped create was one where even he could live a normal life in form, making him feel guilty.
During their new confrontation, the now reformed Bishop saved him when Stockman's hideout was destroyed yet again, when another explosion is triggered by Donatello's sound waves. Bishop tells the now reformed scientist that with the advancement in human technology over the last 100 years, creating a new body (based on his current DNA) for Stockman is very easy. President Bishop subsequently offers Stockman a chance to work for him, as Stockman expects this to be his lackey working in a secret lab. However, he is surprised when Bishop says the Department of Agriculture has expressed interest in his Mousers and he wants him to meet with them. Stockman accepts this offer and asks Bishop if there is a vice president.