Managed to defeat the whole Cochise controlled robot army in that last battle, all the npc helpers that had joined my squad in final battle died during it, even General Vargas our boss.
It's very odd after i looted every corpse that they all had terribly bad weapons with crap armor, no surprise they did so few damage and took so much of it in the face.
Took me some reload to replay the battle as those stupid helping npc never ceased to shoot us in the back with their terrible weapon skills, so in the end i stay behind waiting for those idiots to be exterminated before i could finally get in position.
Oh well, after listening to the overly long last monologue from Cochise , i noticed the main elevator was now out of reach to exit as Cochise had taken over the whole structure and wouldn't let us to get through the oddly computer skill/weapon/explosive impervious door anymore.
Before i could search if there was another exit something in this giant room, the countdown before Cochise managed to spread to every robot outside ended.
Yeah, so worse ending , well bad end for everyone in the outside world as the robots and people with implants are all now Cochise and will progressively kill everyone at some point.
Good end for us, my squad is (well until food and water run out) completely safe from the robots army in the forever locked down Citadel that has no more robots inside