Gordon and Alyx head for Antarctica, resting place of the Borealis, the research ship mentioned at the end of Episode 2. They’re shot down as they approach, though, and find that surrounding the ship is an enormous Combine base, inside which the Borealis is continually flickering in and out of existence.
After an encounter with Dr. Breen—whose consciousness had been transplanted into an alien slug’s body, allowing him to survive the demise of his human body in Episode 2—Gordon, Alyx and Dr. Mossman (who you rescue from a Combine prison) manage to board the Borealis, and while there are pulled across both space and time, seeing things like the Seven Hour War, alien worlds the Combine were about to conquer and even the ship’s origins at Aperture.
Following a dispute over what to do with the ship (Mossman argues for keeping the ship, Alyx wants to honour her father’s wish to destroy it), Alyx shoots Mossman dead, and commits Gordon to a plan to drive the ship into the heart of the Combine’s “invasion nexus”.
Before it can strike, though, the G-Man arrives, speaks with Alyx and the pair depart, leaving Gordon alone to drive the ship on its suicide mission. Just as its about to hit its target, the Vortigaunts open a portal and save Gordon, dropping him on a shore where he isn’t certain of what year it is or how the war against the Combine has ended.
And...that’s where it wraps, Freeman writing “Except no further correspondence from me regarding these matters; this is my final episode.”
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