It has been many years since the resonance cascade disaster at the Black Mesa Research Facility. The membrane of space and time was fractured, leading to the invasion by alien creatures from the Xen dimensional borderworld. Dr. Gordon Freeman, a research associate involved in the accident, ended the offensive by killing the Nihilanth, the powerful entity controlling the enslaved alien beings. In doing so he attracted the attention of a mysterious inter-dimensional bureaucrat, known to some as the G-Man. Gordon was given a choice: work for the G-Man and his ominous employers, or die. Gordon chose life and was suspended outside of time and space.

Gordon is awakened by the G-Man to find himself in an urban center called "City 17”, in what was once Eastern Europe. Earth has changed greatly during Gordon’s absence. The world is under the control of a totalitarian regime known as the Combine, enforced by oppressive Civil Protection police and "transhuman” Overwatch soldiers. The Administrator that controls the globe is in fact Dr. Wallace Breen, once the administrator of the Black Mesa facility. Gordon may have saved humanity from the Xen invasion, but dimensional anomalies remained and were eventually exploited by an even greater alien menace.

The Combine are a force that span many dimensions, enslaving and assimilating world after world. The Earth is merely one of their latest annexations. With every world that is conquered, the Combine are augmented and advanced—and new species are incorporated into their armies and workforce. Beings are forcibly evolved to best suit the needs of the Combine. The Earth’s natural resources are being depleted, human reproduction has been suppressed and humans themselves are transformed into cyborgs and assimilated into the massive inter-dimensional Combine military. The future for humanity looks bleak.

There is still hope. There is a resistance movement against the Combine, led by other Black Mesa survivors including former security guard Barney Calhoun and scientists Isaac Kleiner and Eli Vance. Reunited with his protective HEV suit and aided by Eli’s skilled daughter Alyx, Gordon Freeman embarks on a mission that will take him through city streets, canals, zombie-infested towns, military-patrolled coastal roads and a crumbling prison. With a lot of luck and a massive body-count, he may even make it into the Combine’s mighty Citadel…