I have a theory: what if the scientist seen in the beginning is actually Dr. Hoffmann from the future? What if he went back to that precise moment to retrieve the MC? (I know about the possible temporal paradox but hear me out), we know from the game that the shuttle was supposed to go that route, right near the fight, we know that the MC has 99% connection with the Mech, we know that, basically, the Mech seems to have been built specifically to be used by the MC. What if, in a more distant future, the MC has been able to win the war, hence why he needed to be taken from the past?