Board Thread:General Discussion/@comment-6747658-20130401084750/@comment-1504072-20130417123221

I don't believe it's Gene, simply due to ideological differences. Though Gene was initially allied with Zero in MPO, he ultimately opposed him by attempting to actually nuke the U.S., something that Zero would not have wanted if he was to usurp the American Philosophers' power base. Therefore, it wouldn't make much sense for Gene to (willingly) ally with Cipher, considering that his Army's Heaven was essentially the same as Big Boss's Outer Heaven; an act of rebellion against the Philosophers' (now-Patriots') world order.