Episode Two picks up almost exactly where the previous episode ended. The train carrying Alyx and Gordon is derailed by an explosion, creating a superportal where the Citadel once stood. Alyx and Gordon escape and travel to White Forest, a rebel base, where Dr. Kleiner, Eli Vance, and Arne Magnusson await them.
Early on, Alyx is gravely wounded by a Hunter and survives only thanks to a Vortigaunt. Alyx's healing requires larval extract from an antlion nest. While the Vortigaunts are busy healing Alyx, the G-Man appears to Freeman and explains that he has been watching over Alyx since rescuing her from Black Mesa. He asks Gordon to deliver her to White Forest safely, then tasks the unconscious Alyx with delivering a message to her father: "Be prepared for unexpected consequences." Alyx regains consciousness, the G-Man disappears, and the heroes continue their journey to White Forest.
They soon find a radio tower, where they are attacked by hunters. Alyx attempts to send a warning to White Forest about the attack, but the signal is blocked due to the Advisor's intervention. Wounded in an explosion in his pod, he flies away, and Combine forces immediately rush to his defense. The car pursues the helicopter, and it is only at Station 21 that it is destroyed. There, Gordon destroys an automatic machine gun while Alyx and the rebels repair the car. The heroes encounter another ambush near the hotel, where force fields block their path.
Finally reaching the base, Alyx hands over the data obtained at the Citadel to Dr. Kleiner, and Gordon helps defend the Resistance from a surprise Combine attack on one of the mines. The data reveals the existence of the Borealis, a vessel thought long lost. The Borealis contains teleportation technology, which, according to Dr. Kleiner, could help in the fight against the Combine. Eli, fearing a repeat of the Black Mesa incident, insists on destroying this technology.
Freeman halts the Striders' advance by protecting Dr. Magnusson's rocket so the team of scientists can send a data satellite into orbit. After the battle, the Resistance successfully launches the rocket and closes the superportal. As Alyx and Gordon prepare to depart for the Borealis, they are attacked by Advisors, who kill Eli. Alyx and Gordon are saved by Dog.