So here's what we know:

There are "Alien Eggs" in the game files.

There is a non-FIB UFO over the military base.

There are tunnels under the base

And the is a picture of an egg on the "Mysterious Drawling"

I think that we will would find the alien eggs and possibly one of their ships (as there is one on the drawling) under the base. as for the jet pack, I believe it was a clue to look under the base.