The story is kicked into high gear when an unidentified "super-soldier" military force infiltrates a multi-billion dollar worth aerospace compound, and the government happens to respond by sending in their own Special Military Forces, but lose contact when a rather other wordly signal cuts radio communications.  It's only a few moments later that the entire team has been wiped out, and afterwards, a special classified strike team has been sent in to eliminate any intruder and determine the origin of the signal in order to contain and control the crisis.  And you're part of that team. Where the story progresses from there, is determined by you and your actions, as the player.