Half-Life introduced the world to bespectacled young physicist Gordon Freeman, Ph.D. A simple research assistant at the Black Mesa Research Facility, Gordon is thrust into the center of a cosmic war by a teleportation experiment gone badly wrong. Alien creatures from distant alien hellholes scramble through a shattered dimensional barrier and set about butchering the Black Mesa staff as a prelude to exterminating life on Earth. Government forces quickly arrive to eliminate the alien threat. Unfortunately, their methodical killing spree targets every human witness as well. Thanks to an experimental hazard suit, Gordon is able to navigate this violent confusion of creatures, staff, and homicidal soldiers, finally reaching then destroying what appears to be the monstrous source of the infestation. The victory is short-lived, however. Gordon's heroics catch the attention of a sinister interdimensional bureaucrat. The G-Man, as he's come to be called, seals Gordon in stasis far from Earth, thought, and time itself.

Gordon emerges from the darkness, nearly two decades removed from his last conscious thought. The G-Man has reawakened him, though the briefcase-toting official's intentions are murky at best. Gordon is back on Earth, but it is an Earth marred almost beyond recognition by a succession of alien overlords known as The Combine. Gordon finds himself a powerless, faceless citizen of City 17, a grim metropolis in what was once Europe. Whether through luck or the G-Man's subtle influence, he's soon the center of a burgeoning resistance movement led by rebel scientists from Black Mesa, including Gordon's friends, Drs. Isaac Kleiner and Eli Vance. More importantly, Gordon is reunited with his protective hazard suit. With the help of Vance's daughter, Alyx, and her enormous pet robot, Dog, Gordon embarks on a fugitive journey that pits him against Combine war machines, alien horrors, and the modified human collaborators who enforce The Combine will. Though he is able to rally the resistance into open war against their totalitarian oppressors, Gordon ends up imprisoned in a massive Combine fortress called The Citadel. Here he meets the Combine's traitorous human liaison, Dr. Wallace Breen. Gordon escapes, and with Alyx at his side, puts an end to Breen's treachery by destroying The Citadel's teleport reactor. As the blast engulfs Alyx and Gordon, the G-Man, his mysterious goals apparently satisfied, reappears to once again toss his pawn into timeless cold storage.

Consciousness returns. Gordon and Alyx discover they've somehow escaped both the reactor explosion and the G-Man's malevolent grasp. Before they can ponder their miraculous survival, the crippled Citadel lurches back to life just long enough to initiate a self-destruct sequence. With Alyx at his side, Gordon must flee a city in chaos before the Citadel's final detonation turns City 17 into a toxic, mutant-infested crater.