Three years following Chell's exile to the surface, GLaDOS unearths a dark mystery that had been buried in the confines of the human vault, and with it sets into motion a chain of events that will change Aperture forever. Yet on the surface, in the war torn City 6, Chell is left to protect the facility - her only home - and its secrets from the greedy hands of the Combine.

GLaDOS and Caroline have formed an unlikely allegiance, and together test with the humans from the long lost vault. One Test Subject, however, leads to a terrible discovery, and the dark secrets of Aperture's past are revealed, as is its darker future.