He would take orders from whoever was in charge. Commanding officer sounds about right. Dont make them treat him like an ally though. Make them treat him like crap, like a worthless tool. It would be more realistic showing how he isn't welcome and only used as a tool and a weapon,and also show how deep the brainwashing is, as he wouldnt disagree with them at all, he would just respond with something like "I agree. I am her simply to serve the country. I am simply a tool."