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Following the events of Half-Life 2, Episode One starts out with Gordon experiencing some kind of vision or flashback that shows the explosion of the Citadel's Dark Fusion Reactor. As time stops, several purple glowing Vortigaunts appear and rescue Alyx Vance. The G-Man is then seen walking through the door made of light toward Gordon Freeman. As he opens his mouth to say something, he is distracted by blue lights and is separated from Gordon by another group of Vortigaunts. Several of them surround the G-Man and block him off from Gordon with a blue energy shield. Obviously angered, he straightens his tie and looks at Gordon while saying in an irritated tone: "We'll see...about that." More Vortigaunts then surround and teleport Gordon, in the same manner as Alyx, removing them both from stasis.

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.

Mirror's Edge takes place in an unnamed, gleaming, "Utopian" City where everything is regulated and controlled by the City regime. To transmit information without alerting the government, so called Runners, including the protagonist Faith Connors (model Noelle Lynn), are commissioned.

During the events of the game, a popular politician, Robert Pope, is murdered. Faith and her sister, Kate Connors, are then subsequently targeted by the City Protection Force. While Kate is arrested, Faith manages to escape. As the story progresses, she tries to unravel the circumstances of Pope's murder and to relieve her sister.