According to the source, the sequel would begin with the humans finding out that a emergency distress beacon was broadcast from the aliens moments before their destruction. The signal will undoubtably reach the remainder of their race. Scientists guess that any follow-up attack will take five years to arrive.
In the subsequent five years Earth rebuilds from the rubble and backengineers the alien technology. This new technology picks up signals coming from deep space - a larger strike force is heading towards Earth, intent upon revenge.
As early in development as it is now, only two characters would return in the sequel. The President would begin to suffer and mentally deteriorate as a side-effect of the alien mind-meld he experienced in Area 51. Also returning would be Randy Quaid's son (portayed by Jimmy Duvall), this time as pilot of the new hybrid of
human-alien combat craft in the military.
For five years the Earth prepares a strike force to repulse the second wave. When the moment arrives, the new alien vessel that enters the solar system is even more massive and powerful than the last one - and they're prepared. Earth forces lose their battle in space. The giant ship arrives near Earth and then begins dispatching millions of troops across the world - forcing a land battle. Combat would rage across the globe the like of which Mankind has never experienced before.
That's all supposed to be in the first hour of screen time.