Hey, longtime fan, first-time caller...
After playing the entire HL series back-to-back, it occurs to me that the "Race X" encountered by Adrian Shepard may well be the tip of the spear for the invading Combine.
-They began to show up just after Freeman left for Xen, an event which would have widened the rift in space-time caused by the resonance cascade and thus allowing further breaches and the "portal storms".
-The Combine commonly uses captured races rather than doing their own fighting, so it's entirely conceivable that they would have used a specialized member species to conquer a planet, then move them off-world and use a different set of species to police it.
-The Advisors bear a bit of a resemblance to Race X creatures.
There's probably other connections; let me know what you think