The game takes place in the eve of the Seven Hour War. Fighting against blood shedding synths and frightening aliens, Adrian Shephard has to struggle his way with his fellow comrades from the Phoenix Command, with the main objective of stopping the construction of a Combine Citadel. In his journey he will find what has happened to the world, moments before the Seven Hour War.
Shephard finally meets up with Jake, a decadent survivor who has been guiding our hero through the gloomy sewers using a hacked communication system. They must now struggle for their own survival and at the same time escape from the infested underground of City Fourteen.