Gordon's prisoner pod comes to a stop just down the hall from Breen's office. There to greet him are a pair of Overwatch Elites, who confiscate his Gravity Gun, and Dr. Mossman, who insists that he's better off not struggling.
Mossman escorts Gordon's pod into Breen's office, where the former Black Mesa Administrator is trying to get Eli to understand his point of view, though Eli seems to want none of it. He finally takes notice of Gordon and gloats about how he basically handed himself over to him on a platter, while also telling the Elite carrying the Gravity Gun to set it down on his desk. He then gloats further about how having both Gordon and Eli in his clutches gives him carte blanche to negotiate with the Combine.
Mossman takes this opportunity to insist that the deal he ought to make with the Combine should be to allow him to live and continue his teleportation research under their employ. Breen, however, retorts that Mossman is more than qualified to continue Eli's research herself, and claims Eli's only use at the moment is to convince the Resistance to surrender and cease with the current uprising. Eli still doesn't budge at this, so Breen reveals to him his other captive: Alyx.
Eli begs for Breen to let Alyx go, but Breen remains steadfast with his own offer: convince the Resistance to stand down, or doom all of humanity, his daughter included. One spiteful act of defiance from Alyx later, though, he's made certain that Eli won't take him up on it, and threatens the two of them with relocation to the Combine overworld. He then turns his attention to Gordon and tries to instead persuade him to become a puppet for the rebellion as Alyx and Eli's prisoner pods are whisked out of the room, but Mossman reveals her true colors and uses Alyx's EMP tool to hack the pods' control panel. Breen tries to call for security with a phone on his desk, but Mossman hacks it as well. Mossman then gets to work freeing Gordon from his pod, but Breen, now trying to make an escape with the Gravity Gun in tow, blasts Gordon as soon as he's freed, knocking him out briefly.
As soon as he regains his senses, Gordon accompanies Alyx as the two of them chase after Breen. They find him not far ahead, attempting to negotiate an escape from the Citadel with an Advisor. He notices the duo chasing him down and escapes into a nearby elevator, but forgets the Gravity Gun in his haste. Gordon picks up the gun as Alyx takes notice of the dark fusion reactor just out the window, which she notes is the power source for the Citadel's portal device, which Breen appears to be using for his escape. Alyx is unable to shut down the reactor because Breen has handed control of it to the overworld, so Gordon takes the elevator down to the portal device to personally confront Breen.
So begins the game's final battle, which sees Gordon using the architecture surrounding the portal device to climb up to where the reactor core is, then overload it with a barrage of energy balls, all while Breen yells at him to give up and two Gunships sent in from the overworld try to stop him. Eventually the core is destroyed, and the teleport platform Breen is standing on gives way and takes him with it. Alyx joins up with Gordon to celebrate his victory, but the celebration is short-lived as the core suddenly explodes.
Just before the fireball consumes them, time suddenly comes to a halt and the G-Man appears to commend Gordon for everything he's achieved in the past few days. He adds that there's been some "interesting offers" for Gordon's services that he's been taking into consideration and apologizes to him for his current circumstances not making sense, promising that the situation will make sense to him eventually. With that, he places Gordon back into stasis, bringing the game to a close.
This chapter contains examples of:
- Badass in Distress: Near the end of the game Gordon Freeman gets himself trapped in the bad guy's lair along with Alyx Vance because he stupidly locked himself in a metal coffin. Not that he had any choice.
- Climactic Elevator Ride: The game has Gordon and Alyx ride up an elevator before the final battle. Alyx takes this time to say a few things.
- Dual Boss: The two Gunships summoned from the Combine overworld to stop Gordon during the final battle. Unlike the Gunships at Nova Prospekt, destroying them is completely optional.
- Heel–Face Turn: Mossman, who up until this point was a Double Agent acting to the benefit of the Combine, ultimately sides with the Resistance and stops Breen from banishing Eli and Alyx to the Combine's home world.
- Hypocrite: Breen is usually insistent on calling his superiors "Our Benefactors", claiming that anyone who calls them "the Combine" is small-minded. Here, we finally learn that whenever he's not publicly speaking he calls them exactly that.
- I See Them, Too: Breen refers to Gordon as a pawn whose skills are for lease to the highest bidder, hinting towards him knowing about the G-Man.
- Killed Mid-Sentence: Alyx, until the Episodes showed us otherwise. While Gordon is rescued from the explosion of the Citadel's reactor by the G-Man, Alyx is left at the mercy of the ensuing fireball before she could finish telling Gordon that they ought to motor.
- Sequel Hook: A remark by the G-Man during his closing speech implies Gordon will have his skills put to use in future assignments. The Episodes proved as much — just not in the way the G-Man intended.
- Spiteful Spit: When Breen invokes the image of Alyx's late mother while caressing her chin, she spits in his face and curses him for so much as mentioning her. Eli is nothing short of pleased at her retort.
- There Is No Kill Like Overkill: Hinted at by Dr. Breen in the Combine Teleporter. "You, on the other hand, will be destroyed in every way it is possible to be destroyed, and in some ways which are essentially impossible!"
- You Fool!: Doctor Breen yells this when Gordon Freeman starts breaking the teleporter.
