After previously causing portals to open between worlds, Gordon released a race of aliens from enslavement on Xen and was placed into stasis by a mysterious figure known only as the G-Man.
Meanwhile a race of aliens known as the combine enslaved Earth and is devouring its resources.
Freeman awakens on a train heading for a massive city known only as City 17.
The alien Combine empire watches over its human minions from a massive fortress called the Citadel, within which the human governor is none other than Gordon Freeman's old administrator, Dr. Wallace Breen.
Uniting with the resistance fighters which contain some of his old acquaintances from the Black Mesa research facility (such as Barney Calhoun from Half-Life: Blue Shift), Gordon leads the resistance to free mankind with the help of the creatures he liberated from Xen, and the Antlion controlled with pheromones.
After the fall of the first fortress G-Man places Gordon back into stasis.