My speculation is : that "Cooper" called the crew at the end to rescue MC, after seeing his back while still on the train... It's unclear why he thought what he was doing was somehow justified to begin with, but seeing the metal pieces seemed to shock and upset him, and it was mentioned that he was writting angrily on his gizmo after that. (I think he only realised at that moment that he was "lied to" about how people like the MC are treated at the place or something, but was too deep in the situation already to make a 360 change of course....so he made the best out of his situation....getting some of the money as well.... ) I'm almost positive he will be back close to immediately as an ally.
On another note, I don't think the memories MC has are fabricated. Habitants of the "new world" for example, use swear words from the MC's world, while they themsleves don't even know where said swears originated from in the first palce .Now....This point can only be considered valid , if we can take what "Cooper" said about this as the truth...and i think we can...in order for him to be able to lie so casually about this, or feeling the need to even lie about it... IF MC is indeed living a simulation.... Then "Cooper" must be aware of the "simulations" in great detail, which would require him to be an agent of "the bad guys" instead of a third party delivery boy, as well as seeing the MC being connected to a machine at least once , and that just can't be the case. (1 His reaction to seeing the MC's back was genuen, as it completely changed his mood going forward...2 he has a kind of bad relationship with the "bad guys" met at the end....)I think it's safe to say he was just in need of easy money, and didn't ask as many questions as he should have, taking his jobs......I believe MC was simply kept in a hibernation of some sort (for whatever reason) possibly indicated by MC's long white hair. Perhaps he was kept in a liquid and it dyed his hair?