Ding! got it!
Ok, Nihilanth…fleeing from XEN…yadda yadda yadda…When the portal storm that occurs after Nihilanth’s death occurs, the combine notices it, discovers earth’s existance, and sends in the Race X of aliens through the other portal created by the resonance cascade…and orders the gene worm to hold it open. One Shepherd destroys the Gene Worm…the Combine realizes what a valuble asset the human species can be, and uses the remains of the two portals to launch a full scale attack on Earth, resulting in the 7 Hour War