Half-Life 2 is the sequel to the original Half-Life, taking place decades after the events in the first game. At the start of Half-Life 2, the G-Man speaks to Gordon Freeman as part of a hallucination-like vision, telling him that his "hour has come again." Freeman then finds himself out of stasis, in a world twenty or so years after the events of Half-Life, and riding a train into City 17, unarmed and without his H.E.V. suit. Details begin to slowly emerge: City 17 (as well as the rest of the world) is under the rule of a totalitarian administrator named Doctor Wallace Breen, the former administrator of the Black Mesa Research Facility. However, Breen is merely a puppet head of state who is carrying out the will of the alien rulers known as the Combine. Attracted to the planet by the portal storms, the Combine mounted a brutal assault on humanity, in which the forces of Earth were completely overwhelmed in the Seven Hour War. The Combine now has near-absolute control over the entire planet, with only a few pockets of human resistance remaining. Doctor Breen enforces his rule (and, by extension, the Combine's rule) through armies of Civil Protection units (also called "Metropolice" or "Metrocops") and Combine soldiers (referred to as the Overwatch).
Chapter 1: Point Insertion
Once Gordon disembarks the train, he eventually meets up with his old friend and co-worker from Black Mesa, Barney Calhoun, who has infiltrated the Civil Protection in support of the fledging resistance movement. Barney instructs Gordon to make his way to Doctor Isaac Kleiner's lab, but along the way, Civil Protection detects Gordon and he is put to flight. Surrounded and eventually stunned by the Civil Protection, Gordon is rescued by Alyx Vance, the daughter of Doctor Eli Vance.
Chapter 2: "A Red Letter Day"
After rescuing Gordon from the Civil Protection, Alyx Vance brings Gordon to Doctor Kleiner's lab. After Gordon is outfitted with his upgraded H.E.V. suit, Doctor Kleiner attempts to teleport Alyx and Gordon to Black Mesa East, where Alyx's father is waiting. Although Alyx makes it to Black Mesa East, Doctor Kleiner's pet headcrab Lamarr pulls off a crucial wiring as she falls from a ventilation shaft, when Gordon is in the process of being teleported. The interruption leads to a chaotic sequence in which Gordon is briefly transported to, in addition to other locations, the office of Doctor Breen at the Combine Citadel. He eventually ends up outside Kleiner's lab, where Barney gives Gordon his old crowbar. The Citadel is on high alert for Gordon, and Barney tells him to take the canals to get to Eli's lab.
Chapter 3: Route Kanal
While navigating the city's canals, Gordon is chased by Civil Protection and scanners. He finds small resistance bases populated by both humans and Vortigaunts, one of the several species of invading aliens of the original Half-Life turned allies. After being helped through an underground railroad system, Gordon is provided an air boat, allowing him greater expediency.
Chapter 4: Water Hazard
Gordon's air boat is soon spotted by the Combine and relentlessly pursued by a hunter-chopper assault helicopter. At another resistance base, a Vortigaunt affixes a salvaged Overwatch hunter-chopper turret to the craft, which allows Gordon to eventually down the pursuing helicopter.
Chapter 5: Black Mesa East
Gordon eventually arrives at Black Mesa East and meets Doctor Eli Vance and Doctor Judith Mossman, as well as rejoining Alyx. Alyx gives him a tool originally developed for handling hazardous materials called the Zero-Point Energy Field Manipulator (also known as the gravity gun) and instructs Gordon on its use while also introducing Dog, Alyx's pet robot. In the middle of playing "fetch", the lab is attacked by the Combine, and while trying to get to the lab Eli was in, collapsing debris separates Alyx and Gordon, forcing him to escape along an old tunnel leading to Ravenholm. Alyx and Dog escape by unknown means while Eli and Mossman are captured by the Combine.
Chapter 6: "We Don't Go To Ravenholm..."
Gordon quickly discovers why Ravenholm was abandoned: the town was shelled with containers containing headcrabs by the Combine, causing Ravenholm to be overrun with headcrabs and zombies. Father Grigori, a seemingly unstable priest and likely the last human resident of Ravenholm, helps him survive the deadly town by giving Gordon advice and killing many zombies and headcrabs himself and escorts him to an abandoned mine which eventually leads to the dockyards and the coast outside City 17. Gordon then finds another resistance base under assault by Combine troops. After dealing with the attackers, a rebel leads Gordon to a radio where Alyx has been contacting them. Alyx tells him that Eli has been captured and is being held in Nova Prospekt, an old maximum-security prison turned into a factory where the Combine creates Overwatch Soldiers and Stalkers.
Chapter 7: Highway 17
Gordon must make his way to Nova Prospekt. Aided by a tau-cannon armed dune buggy, he travels across Antlion infested beaches and Combine controlled outposts. During this journey, Freeman successfully accomplishes many feats including downing multiple gunships and disabling a combine controlled bridge.
Chapter 8: Sandtraps
Gordon's journey to Nova Prospekt continues on foot after he leaves his dune buggy in a garage. Previously, Gordon aided a resistance outpost called Lighthouse Point. There he defeated numerous attacks by the Combine. he encounters Antlions, which are hidden underground and emerge to attack at the slightest footstep on sand. Gordon must stay on the rocks scattered on the beach to avoid encountering many antlions. After defeating an enormous Antlion Guard near another resistance base, a Vortigaunt extracts a pheropod (aka pheromone grenades or bugbait) from the dead creature. Giving it to Gordon, he informs him that this gland can pacify the smaller Antlions and allow Gordon to command them. With a squad of antlions to help him, Freeman makes a frontal assault on the former prison dubbed Nova Prospekt.
Chapter 9a: Nova Prospekt
Invading Nova Prospekt with an army of Antlions, Gordon fights through the prison and searches for clues to Doctor Vance's whereabouts. The Antlions' assistance helps to even the overwhelming odds against him.
Chapter 9b: Entanglement
Gordon meets up with Alyx again, and together they find both Eli and Doctor Judith Mossman, the latter found to be a Combine spy. The four meet at a Combine teleportation room, preparing to return to Kleiner's lab. While Gordon and Alyx are distracted by an alarm set off by Mossman, she teleports herself and Eli into the Citadel, the Combine's base of operations. After holding off a large group of Combine soldiers, Gordon and Alyx barely manage to teleport themselves to Doctor Kleiner's lab before the teleporter explodes, but a malfunction in the equipment causes them to arrive at Doctor Kleiner's lab a week after they teleported.
Chapter 10: Anticitizen One
In the previous week, news of Gordon's successful invasion of Nova Prospekt has brought new life to the citzens of City 17, causing them to rise up in armed rebellion, with Barney leading the Resistance in an effort to reach the Citadel and free Eli Vance. Resistance fighters led by Freeman travel towards the Citadel to join up with Barney and 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 she is subsequently captured by Combine forces. Gordon is then forced to travel through an abandoned industrial complex to reach Barney.
Chapter 11: "Follow Freeman!"
After reaching Barney, the pair fight their way to the "Nexus Building". Gordon shuts down a suppression device blocking access to the Citadel, while Barney stays to help resistance members. Outside, a pack of powerful Combine war-machines, the Striders, attack until they are destroyed by Freeman and numerous rebels.
Chapter 12: Our Benefactors
After fighting through a heavily damaged area of the city, Gordon enters the Citadel through an underground passage with the help of Dog. Faced with a dead end, he is forced to enter a rail-driven containment apparatus. After a long trip through the Citadel, all his weapons are destroyed or removed by a dark energy-powered "confiscation field." However, the gravity gun absorbs the energy from the beam and shorts it out. It can now manipulate organic matter, instantly kill Combine forces, destroy their weapons and lift objects several times more massive than previously able. Gordon's HEV suit is also affected, as it is now able to withstand more damage and work more efficiently. Armed with only the gravity gun, Gordon wreaks havoc upon the Citadel, fighting a large number of Combine forces and even a strider until he is again faced with another dead end. Once more, the only way to progress is to voluntarily enter a containment apparatus, which brings him face-to-face with Doctor Breen.
Chapter 13: Dark Energy
Arriving at Doctor Breen's office near the top of the Citadel, Gordon's gravity gun is taken while Gordon is immobilized. Doctor Judith Mossman is with Breen, and he summons Eli and Alyx, who are being held in similar devices. During this period, Breen makes a very notable statement towards Freeman: Freeman's contract "was open to the highest bidder," suggesting that Breen is aware of the G-Man and his influence over Freeman. After unfriendly exchanges of dialog with Eli and Alyx, and with desire to discuss with Freeman person-to-person regarding Freeman's "contract", Breen prepares to initiate the teleportation of both Eli and Alyx to the end of a Combine portal.
As Breen threatens the Vances, Judith finally turns against him, fed up with Breen's treatment of Eli. Seeing that Breen intends to hand Eli and Alyx over to the Combine, she shuts down his computers and frees the three captives. Breen manages to escape through a nearby elevator, and flees towards a huge "Dark Energy Reactor" at the top of the Citadel, intending to teleport 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. At the instant the explosion occurs, the G-Man seemingly "stops time," saving Gordon from the ensuing blast. The G-Man appears, congratulates Gordon, and mentions that he has received several offers for Gordon's "services," before placing him once again into stasis. However, it is still unclear who hired Gordon Freeman, and his exact mission. After the G-Man retrieves Gordon, and walks through a door of pure light, the game ends exactly as it began, in darkness.
Half-Life 2: Episode One resumes the series' storyline from this point on.