The objective (mostly) is to gather scraps of technology. The mech being the most prised tech as every part of it is a computer and they have a http://en.wikipedia.org/wiki/ARPANET Arpanet and in the spirit of that every networked military computer has a complete copy of all the military files.
So every part has some salvageable information.
Along the way you meet up with two very strange people who seem interested in helping but only so there children make rule.
Eventually you find the children of those who were slaughtered (maybe insane?) then you find they are the only survivors of the race who worshiped the creators of the void and near godlike in abilities themselves.
In the final level the bad guys have made a paradox machine that makes it possible to change time with out having the resulting paradox nullify the results.
They have the paradox machine powered up so you can't touch it with out being paradoxed out of existence but the controls are outside the paradox effect so smash the controls and win.
Then the strange man and woman show up and nothing stops them from entering the paradox effect not even the knowledge that it will erase them from existence.
They paradox there own race back to life at the price of there own existence.

They are gone, The group had so many questions but now it'll be imposable to get an answer. Or so they think as the player picks up the control computer one of the two carried into the paradox leaving the question if it survived maybe so did they.