Metal Gear Solid - HD Walkthrough Part 13 - Metal Gear REX Boss Fight - No Commentary 

Snake has been used by Liquid and entered the detonation code. Snake, mad at the fact that he was used, is told by Liquid of an even more shocking fact. The Pentagon's goal from the beginning was to assassinate the terrorists, and others involved with Fox Die, carted by Snake, to hide the facts about the development of Metal Gear. Liquid also tells Snake that they are twins.
While Snake is shocked from what he has been told, Liquid finally starts controlling Metal Gear...