The covert operation team known as FOX-HOUND takes over a nuclear weapon disposal facility, they threaten to fire nuclear weapons at the united states if they do not give them the remains of Big Boss. But things don't go as they had originally planned and they can't activate the stealth missile launchers, which is why they let Snake infiltrate their base. Liquid also has an ulterior motive, he wants to get revenge on Snake. They were both cloned from Big Bosses DNA, and Snake got all the good stuff while Liquid got the bad stuff. Big Boss always said that Snake was the good one, his favorite.