They go to Antarctica to find the Borealis (the ship built by Aperture Science from Portal).
The Borealis is phasing in and out of reality. Rescue Dr Mossman from the Combine, she has details to make the Borealis phase in for enough time to get Freeman+Alyx+Mossman on board, chased by Combine.
While on board, discover Borealis is moving through Time as well as Space. Mossman wants Borealis recovered for the Resistance, Alyx wants it destroyed. They fight, Alyx kills Mossman.
Borealis reconfigured to fly through Space to Combine planet to try to destroy it with explosion, as they arrive G-man takes Alyx off the ship, Vortigaunts take Freeman.
Combine world too massive, powered by a Dyson sphere, Borealis explosion does nothing.
Freeman back on Earth sometime in the future, won't take part in any more conflict with Combine.
I haven't played the game, so I'm a bit confused: what parts of the story are slyly referring to Valve itself rather than the HL3 story? How do you get "welp, looks like HL3 is cancelled" based on this story?
The last paragraph is almost definitely about Valve:
"And here we are. I spoke of my return to this shore. It has been a circuitous path to lands I once knew, and surprising to see how much the terrain has changed. Enough time has passed that few remember me, or what I was saying when last I spoke, or what precisely we hoped to accomplish. At this point, the resistance will have failed or succeeded, no thanks to me. Old friends have been silenced, or fallen by the wayside. I no longer know or recognize most members of the research team, though I believe the spirit of rebellion still persists. I expect you know better than I the appropriate course of action, and I leave you to it. Expect no further correspondence from me regarding these matters; this is my final episode."
No more HL2:Episode N coming, the development team is too different.
The Borealis is phasing in and out of reality. Rescue Dr Mossman from the Combine, she has details to make the Borealis phase in for enough time to get Freeman+Alyx+Mossman on board, chased by Combine.
While on board, discover Borealis is moving through Time as well as Space. Mossman wants Borealis recovered for the Resistance, Alyx wants it destroyed. They fight, Alyx kills Mossman.
Borealis reconfigured to fly through Space to Combine planet to try to destroy it with explosion, as they arrive G-man takes Alyx off the ship, Vortigaunts take Freeman.
Combine world too massive, powered by a Dyson sphere, Borealis explosion does nothing.
Freeman back on Earth sometime in the future, won't take part in any more conflict with Combine.