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Private Notes
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 and Dr. Kleiner through a portable monitor, to inform them that Gordon is safe (Eli earlier told Alyx that Gordon wouldn't be found, implying his knowledge of the G-Man and his stasis). 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.
This chapter consists of Gordon Freeman entering the core to help slow down the meltdown. Afterwards, they make their way to one of the still running Razor Trains and begin their journey to escape the city.
Alyx is trapped under a pod with a restrained Stalker viciously attempting to break loose, relying on Gordon to set her free. After escaping from the train, the duo fights through the rubble of dark, deserted, underground parking garages and tunnels, searching for a way to head up to the surface of the city. In the process, they block off Antlion burrows, and battle various zombies in a pitch black environment, including zombified Combine soldiers, which were never seen during Half-Life 2. These zombified soldiers, referred to as "Zombines" by Alyx, are a prominent sign that the Combine is losing control of City 17.
Eventually, the duo manages to find the exit of an underground train station and Gordon and Alyx come up to the surface, observing the citadel from afar, and the destruction already visited on City 17. Dr. Kleiner appears on the screens that Breen used to pass out propaganda, mentioning that the Suppression Field, which had previously prevented human reproduction, is down. As the duo moves on, they engage in several fights with Combine soldiers, Antlions, and zombies.
Alyx and Gordon finally 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 to draw the remaining Combine forces away from the refugees. Inside the hospital, Combine forces and zombies of all kinds are fighting throughout the collapsing structure, and hastily constructed defences to slow Alyx and Gordon down.
Upon reuniting with Barney at the train station, Alyx and Gordon work to move several groups of citizens to the trains while facing increasing Combine opposition.
After battling Combine soldiers and a Strider, the duo reprogram another train and board the caboose. As the train carries Alyx and Gordon away, the Citadel is visible in the background with the reactor core once again about to explode. Several pods are ejected from the Citadel as it detonates. On two occasions, as pods pass overhead, Gordon and Alyx are hit with psychic blasts. The force of the shockwave from the exploding Citadel causes metal chunks and wreckage to fly toward the train Alyx and Gordon are on as it sends its final transmission, and the screen fades to an ominous white as the Citadel explodes, destroying City 17, and causing a shockwave that overtakes the train. The last thing that the player hears is the twisting of metal and Alyx whispering Gordon's name. The screen then fades to the credits.
