Board Thread:General Discussion/@comment-10941901-20130723221328/@comment-10941901-20130724005406

Think, Foxhound was built on opposition of Fox, the unit Big Boss was with when he worked alongside Zero, which might have made it take longer for the Patriots to develop an influence over the group. Big Boss would probably be welcomed back with open arms too, if the Patriots haven't sunk their talons into Foxhound.

Or instead, maybe the Patriots have got control of Foxhound, but keep it from Big Boss so he THINKS he has control. Kojima loves his twists and dirty little (plot) secrets, and so do we.