Five years prior to
Gordon Freeman's arrival to City 17, Alyx (Ozioma Akagha) and Eli Vance (James Moses Black) are on a mission to steal a reactor from the Combine. However, Eli catches sight of a strange structure in City 17's Quarantine Zone, which triggers a massive manhunt by the Combine that results in the capture of both Alyx and Eli. Another Resistance member, Russell (
Rhys Darby), manages to rescue Alyx and warns her that the Combine will transport Eli to Nova Prospekt for interrogation. Taking a pair of Gravity Gloves from Russell, Alyx ventures into the Quarantine Zone to intercept the train carrying Eli. Along the way, she meets an eccentric Vortigaunt (
Tony Todd) that warns her Eli will die in the future.
After making her way through the Quarantine Zone, Alyx is able to derail the train. The Vortigaunt rescues Eli from the wrecked train and Eli warns Alyx that while in custody, he learned that the Combine are storing a superweapon called the "Vault" in the Quarantine Zone. He instructs Alyx to find the Vault and steal it before the Combine can move it to a safer location. On her way, she helps a human survivor Larry (
Rich Sommer) defeat a mutated alien monster nicknamed "Jeff". She then descends into a network of Antlion tunnels. Eli then gets into contact with Alyx and warns her that the Vault isn't a weapon, but is in fact containing something that even the Combine fears. Alyx continues on, reasoning that whatever is inside can help them fight the Combine.
Upon getting closer to the Vault, Alyx overhears a Combine scientist (
Kim Dickens) say the Vault contains a survivor of Black Mesa. Eli believes that Gordon Freeman is being held within the Vault, and tells Alyx it is of utmost importance that he is freed. Alyx fights her way through the Combine security forces and enters the Vault. Inside, she finds a high tech cell and opens it, but instead of finding Gordon, she ends up releasing the G-Man (
Michael Shapiro) from Combine imprisonment. The G-Man thanks Alyx for freeing him, and offers his services. Alyx asks for the removal of the Combine from Earth, but the G-Man replies that request is beyond his power to achieve. However, the G-Man instead offers Alyx the chance to save Eli, and shows her the future event where
Eli is killed by a Combine Advisor. Alyx uses her Gravity Gloves to kill the Advisor, saving Eli and changing his fate. However, the G-Man then points out that Alyx has proved herself capable of replacing Gordon, who the G-Man has grown dissatisfied with due to Gordon being unable or unwilling to carry out his given mission. The G-Man then leaves, trapping Alyx in stasis.
In a post-credits scene, Gordon regains consciousness in the Resistance's White Forest base and finds Eli alive from the Advisor attack but Alyx missing. Eli becomes furious when he realizes that the G-Man must have taken her. The G-Man can be seen watching from the far left of the warehouse. Dog arrives with Gordon's crowbar, which Eli returns to Gordon and tells him that they "have work to do.