The story begins with Lara's teenaged tomb raiding origins, accompanied by her former mentor Werner Von Croy. They travel to the temple of Angkor Wat, Cambodia in the hope of finding the mystical "Iris." However, the trip is cut short by an accident where Lara is forced to abandon her companion in order to save her own life. Back in modern day Egypt (the entire game takes place in one country, unlike other installments in the series), Lara Croft uncovers an ancient tomb where a fearsome Egyptian God was once imprisoned.

She unwittingly unleashes him and finds herself in a deadly race against time to restore the god to his resting place before an apocalypse befalls Earth. Unfortunately, Von Croy becomes Lara's new rival as he is possessed by Set himself and he makes things considerably more difficult.