Oh, what happened to him?

He's become a little bit of a pet project for Enjoi and Alacrity, the two being the most tech savvy and the former knowing how the primordial ooze works.

They found out that he was defeated and went to make sure. They discovered an unfinished backup robot body, with no means of escape or interaction with environment and hooked up to the wires that would keep it powered and conscious.

They took it and obviously didn't finish the robot body, instead hooking him up to an isolated computer so he couldn't corrupt more tech, and to observe his mental state and coding. He can shut down to rest if he wants and talk to visitors.

Alacrity argued that to change some people, they have to hear the right thing. So they're making sure the commander has no bad intentions before they do anything more with that idea.