Nonsense! There's so much room for possibilities. The Borealis was an Aperture invention, and HL2:E2 ends with the search for it. The setup is there for a Portal / HL crossover episode.

And Chell doesn't have to make an appearance. We know of at least 1 other surviving subject from Portal 1 and Portal 2 opens with Wheatley relocating subjects in the same form of stasis Chell was put in. Plus >!the subjects that the robots discover!< at the end of P2. Maybe there's >!more vaults, and maybe they could make an army!<? And you got the cores that can talk and some that seem to have AGI...

But honestly you don't even need any intelligent beings. Aperture itself stayed safe ostensibly for >9,999,999 years after the war, and many years before it. Parts of Aperture could serve as a hideout, especially if they find the Borealis to get in and out of there without a trace. Laidlaw said in his Epistle >!that the intention was to use it for combat!<, but I don't see why they couldn't spelunk Aperture for some weapons and tools first.

All it takes is one pair of moon dust panels to drain an entire planet's atmosphere of whatever an alien needs to survive on their planet, and more could do it faster... Or maybe they could tinker with the portal guns to shoot bigger portals while Gordon goes on a side quest or something. Then tele in on the Borealis, set up an array of panels and portals, tele out and open the corresponding portals from a distance in space. There's your climax of the episode, important Combine planet #1 is in peril and while Earth is probably in danger of a counter-strike (hehe), they're in an even better position to respond and defend than they were before.