Board Thread:Questions and Answers/@comment-26632572-20160219142916/@comment-1504072-20160219173752

MSF was a threat to Skull Face, just as it had been to Cipher previously. He allied with the Soviets in Afghanistan to build Sahelanthropus, before betraying them. XOF is a rogue shadow group, so of course U.S. groups would oppose them. Ocelot assisted Big Boss out of admiration/friendship, while maintaining ties to the Patriots and working from within the group to ultimately fight against it.

Seriously, you should play the games, you will get a much better understanding than any simplified answer given here.