At the start of the game, the G-Man speaks to Gordon Freeman as part of a hallucination-like vision as he is pulled out of stasis and placed on a train. Gordon exits the train to find that the world has been overtaken by an extradimensional military force known as the Combine. Gordon meets up with Barney Calhoun and sets out for Doctor Isaac Kleiner's lab while being chased by Combine Civil Protection, meeting Alyx Vance along the way. Once they reach their destination, Kleiner attempts to teleport them to Black Mesa East, but although Alyx arrives successfully, Kleiner's pet headcrab, Lamarr, damages the device when Gordon tries to use it. Gordon is thus briefly teleported to many places, most notably Dr. Breen's office, who alerts the Combine to his reappearance. He finally materializes just outside the window of Kleiner's lab. Barney instructs Gordon to take the city's canals to get to Black Mesa East, where Alyx's father, Dr. Eli Vance, works.
While navigating through the city's canals, Gordon is chased by the Combine on foot until being supplied with an air boat at a rebel outpost; by this point it becomes increasingly obvious that Gordon has a heroic, almost messianic reputation with the rebels and outlaws. However, the air boat is soon spotted by the Combine and pursued by a hunter-chopper assault helicopter. Using a salvaged hunter-chopper turret, Gordon manages to take down the pursuing helicopter.He arrives at Black Mesa East and meets Eli Vance and Doctor Judith Mossman, also rejoining Alyx. Alyx gives him a tool originally developed for handling hazardous or heavy materials called the Zero-Point Energy Field Manipulator (also known as the gravity gun) and instructs Gordon on its use while also introducing Dog, her giant “pet” robot. The lab is attacked by the Combine, Alyx makes it safely back to the lab, but Gordon is forced to escape along an old tunnel leading to Ravenholm.
A Combine shelling has caused Ravenholm to be overrun with headcrabs and zombies. The last survivor, Father Grigori, the half crazed church pastor, helps Gordon through Ravenholm and ultimately leads him to the dockyards outside City 17.Freeman is alerted by Alyx via radio that Eli has been captured and is being held in Nova Prospekt. Gordon travels to Nova Prospekt in a dune buggy, helping to down a Combine gunship after meeting Colonel Odessa Cubbage at another resistance base. The journey is made difficult due to Antlion infestation along the coast, but once Gordon kills their Antlion Guard master, the Vortigaunts are able to extract pheropods which Gordon can then use to control a number of antlions in the assault on Nova Prospekt.
At Nova Prospekt, Gordon searches for Eli. Alyx joins with Gordon again, and together they find both Eli and Doctor Judith Mossman (revealed to be a Combine spy). Mossman creates a distraction and teleports herself and Eli into the Citadel, while Gordon and Alyx teleport themselves to Doctor Kleiner's lab. A malfunction in the equipment causes a huge explosion, which causes the time to slow down during the teleportation, contracting seven days into a few seconds. They arrive at Doctor Kleiner's lab a week after they left Nova Prospekt. During this lost week, the explosion has been taken as a signal to start the resistance, which has considerably strengthened, turning City 17 into a warzone. Gordon leads freedom fighters towards the Citadel to free Doctor Vance while Alyx helps Doctor Kleiner escape the lab. Later, Alyx briefly rejoins and accompanies Gordon in a battle to disable a Combine power generator, but is subsequently captured by Combine forces. After reaching Barney, Gordon shuts down a suppression device blocking access to the Citadel and brings down a pack of Striders.
Gordon enters the Citadel through an underground passage. All of his weapons are destroyed by a “confiscation field”, except for the gravity gun. An unexpected reaction with the confiscation field causes the gun's powers to be amplified, and using this Gordon wreaks havoc upon the Citadel. Gordon enters a containment apparatus, which brings him face-to-face with Doctor Breen. Doctor Judith Mossman is with Breen, and he summons Eli and Alyx, who are being held in similar devices. During the confrontation, Breen remarks that Freeman's services are “open to the highest bidder.” As Breen threatens the Vances, Judith turns against him. Breen manages to escape to a “Dark Energy Reactor” at the top of the Citadel with the intent of teleporting himself away from Earth. Gordon and Alyx pursue him, and Gordon destroys the reactor, both to depower the Citadel and to prevent Breen's escape. This triggers a massive explosion in which Alyx and Gordon are imperiled. However, at the moment the reactor explodes, time stops. The G-Man emerges, commenting on Gordon's successful endeavors. He places Gordon back into stasis and leaves through a door of pure light.
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