Following the events of Half-Life 2, Episode One starts with Gordon experiencing some kind of vision or flashback that shows the explosion of the Citadel's Dark Fusion Reactor. As time stops, several purple glowing Vortigaunts appear and rescue Alyx Vance. The G-Man is then seen walking through the door made of light toward Gordon Freeman. As he opens his mouth to say something, he is distracted by blue lights and is separated from Gordon by another group of Vortigaunts. Several of them surround the G-Man and block him off from Gordon with a blue energy shield. Angered, he straightens his tie and looks at Gordon while saying in an irritated tone: "We'll see...about that." More Vortigaunts then surround and teleport Gordon, in the same manner as Alyx, removing them both from stasis.
Gordon wakes up outside the Citadel, buried under a pile of rubble. Dog digs Gordon out and he is reunited with Alyx, who embraces him. She contacts her father, Eli Vance, and Dr. Kleiner to inform them that Gordon is safe. Kleiner tells Alyx that the Citadel Core is at risk of exploding at any moment. Kleiner states that the explosion could be large enough to level the whole of City 17 and that the only possible way to survive would be to re-enter the Citadel and slow the core's progression toward meltdown. Eli interrupts, showing distress at placing his daughter in further danger, but reluctantly agrees when he sees no other option. Alyx and Gordon re-enter the Citadel to try to reactivate the stabilization mechanism for the core in order to avert disaster.
During the pair's time in the Citadel, they discover a recording of the discussion between a Combine Advisor and Dr. Breen before his confrontation with Gordon in Half-Life 2. Breen reprises his words, saying:
"It's me you should be worrying about. I can still deliver Earth, but not without your help... The portal destination is untenable, surely you can set the relay elsewhere. There's no way I can survive in that environment... A host body?! You must be joking! I can't possibly- Oh alright, damn it! If that's what it takes. Just hurry, he's right behind me! Oh shit!"
The recording ends, interrupted by a brief image of a Combine Advisor. Alyx and Gordon are then subject to psychic blasts as an Advisor pod is transported through a tube in the control room. They then proceed down a glass elevator to the Citadel Core.
