With how HL: Alyx changed up Ep2's ending, it's hard to say. I guess Ep3 would be about getting Alyx back, as well as working towards getting to the Borealis before the Combine.

I assume you meant HL3 would be after Ep3. In that case, that makes things even harder to consider. If we go by how Mark Laidlaw set everything up at the end of Epistle 3, then we get into the realm of pure speculation.

If I had to assume, HL3 would take place when the resistance is rebuilding society. Maybe the G-Man and his benefactors would lash out and try to reclaim Gordan, Alyx, and ect as assets for their personal use. Past that, I have no idea.