Half-Life 2: Episode One is the direct continuation of Half-Life 2, which ends in a climax where Gordon Freeman successfully leads an assault on the Earth-occupying Combine, and is returned into stasis by the G-Man, leaving Alyx Vance in the verge of death in a large explosion at the top of the Citadel.
During the start of Episode One, Alyx Vance is seen standing motionless as a huge explosion is about to expand behind her. Several Vortigaunts teleport in and rescue her just before the explosion of the "Dark Energy Reactor" occurs. Afterward, Gordon Freeman sees the G-Man coming back into his cold storage. The G-Man is about to say something, but then finds several Vortigaunts holding him back from Gordon. Two Vortigaunts carry Gordon away while the G-Man says, "We'll see... about that!"
Chapter 1: Undue Alarm
Gordon awakes under a pile of rubble at the base of the burning Citadel. Dog picks Gordon out of the rubble where Alyx is ecstatic to see him. She embraces him, tells Dog to give Gordon the gravity gun (which has returned to its normal state), and explains that she doesn't remember how they survived the explosion. All she remembers is, "Breen falling, huge explosion, and then I heard Vortigaunts..." Suddenly a message from Doctor Eli Vance comes in and Gordon, Alyx, and Dog rush over to hear it. Dr. Isaac Kleiner and Dr. Eli Vance explain to Alyx that the Citadel's core is at risk of exploding at any moment. Dr. 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 towards 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.
Chapter 2: Direct Intervention
With the help of Dog, who sends Gordon and Alyx into the Citadel by tossing a van that seats the duo, the two reach the core of the Citadel to reactivate the stabilization mechanism for the core, averting disaster.
During their time in the Citadel the gravity gun is altered to be able to manipulate organic matter once more, and Gordon and Alyx discover a recording of the discussion between a Combine Advisor and Dr. Breen before Gordon chased him down in Half-Life 2. Breen says,
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 all right, damn it! If that's what it takes. Just hurry, he's right behind me! Oh shi-
The recording ends, interrupted by a brief image of a Combine Advisor. Alyx and Gordon are then subject to a small psychic blast as an unknown vessel containing what looks like a Combine Advisor being transported through a tube in the control room, where other Combine Adviors in pods remain. Gordon and Alyx are successful in re-engaging the reactor's containment system, delaying the explosion. Alyx subsequently discovers that the Combine are trying to use the reaction, and therefore the destruction of the Citadel, to send a message to off-world Combine forces. She makes a copy of the message packet to take to Dr. Kleiner and Eli, ensuring that the Combine make them their prime target and even in their disorganized state attempt everything they can to stop them.
Alyx and Gordon then board a Razor Train to escape the Citadel. It becomes apparent that the carriage which Gordon and Alyx are in is being used to transport Stalkers. Alyx mourns for the Stalkers and is then interrupted by the train derailing, which wakes the Stalkers. Alyx is trapped under a pod with a restrained Stalker viciously attempting to break loose, relying on Gordon to set her free.
Chapter 3: Lowlife
After escaping from the train, the duo must fight through the rubble of dark and deserted underground parking garages, tunnels and blocking off Antlion burrows and fighting headcrab zombies and Zombines in a pitch black environment, while finding a way to go up to the surface of city. Eventually, the duo manages to find the exit of underground train station and reach to the surface.
Chapter 4: Urban Flight
Dr. Kleiner is now shown on the screens that Breen used to pass out propaganda, and mentions that the suppression field, that had previously prevented human reproduction, is down. Gordon and Alyx come up to the surface, observing the Citadel from afar, and the destruction of City 17 scenery. As the duo moves on they engage in several fights with Combine soldiers, Antlions, and various zombie forms.
Alyx and Gordon eventually meet up with Barney Calhoun and a group of other survivors who are preparing to move on a train station in order to escape City 17. With the Combine still following, Gordon and Alyx split up from the group and move through a derelict hospital so as to draw the remaining Combine forces away from the refugees.
Chapter 5: Exit 17
Upon reuniting with Barney at the train station, Alyx and Gordon work cooperatively to move the citizens to the trains, while facing increasing Combine opposition. They then decide to stay behind to lure the Combine away from Barney and the citizens as they board the train and make their escape.
After battling Combine soldiers and a strider, the duo reprogram another train and board the caboose. As the train carries Gordon and Alyx away, the Citadel is seen in the background with the reactor core once again about to explode, and the Combine's message is sent. Several pods similar to the one containing the Combine Advisors in the control room are ejected from the Citadel as it detonates. They scatter and fly in random directions away from the Citadel, two of them passing overhead. As each does so, Gordon and Alyx are hit with another red psychic blast. The force of the shockwave from the exploding Citadel causes metal chunks and wreckage to fly toward the train Gordon and Alyx are on as it sends its final transmission, and the screen fades to an ominous white as the shockwave overtakes the train. The last thing that the player hears is the twisting of metal and Alyx's faint voice, calling out Gordon's name.