The game starts as the last one ends, with Philip sending the 'kill them all' message. As soon as he finishes, one of the Infected barges in and hits Phillip on the head with something unseen. The player then controls a character in some kind of tomb. Items need to be collected in each chamber in order to move on to the next. In the journey, the player starts to see familiar places from other parts of the facility and begins to receive communications from persons who Philip had encountered previously, such as Dr. Richard Emminis who Philip encountered in the Computer Room of Black Plague, a member of the Archaic Elevated Caste called Ellof Carpenter, as well as person who later identifies himself as Philip's former adviser, Red, from the first Penumbra game.