IllegalPaladin on 15 June 2008
As others have said, the control stems from the nanomachines and people with nanomachines (mainly registered PMC people) have them and are thus under the control of the system.
If you remember in MGS, Naomi locks Snake from using his weapons through his nanomachines in the nuclear disposal room and she also used the nanomachines to dull Snake's pain in the jail cell after he was tortured by Ocelot. Also, in Act one, he is unable to shoot that M4 at first which required Drebin to give him some new nanomachines. Even if he has older nanomachines, they can still control him.
