In 1945 in New Mexico, a blast from a nuclear experiment in Manhattan Project reveals a strange crystalline structure, from which a winged creature flies out. In Calcutta 1996, Lara Croft is approached by Larson Conway, who introduces her to Jacqueline Natla, who wishes for Lara to find a piece of an artifact called the Scion, located in the Peruvian mountains. Lara, having searched unsuccessfully for such an artifact with her father in the past, agrees to go.
In the Peruvian mountains, Lara finds a tomb belonging to god king Qualopec. She discovers that he was one of three God Kings (the Triumvirate) who ruled Atlantis before it sank. Lara leaves with a piece of the three-part Scion, but notices movement from what had appeared to be a statue of Qualopec before the tomb collapses. Shortly after, Lara is confronted by Larson, who attempts to take the Scion piece from her. After knocking him out, she discovers that Natla has sent Pierre Dupont, another archaeologist, to find the next piece. Lara breaks into Natla’s office that night and finds evidence that the next piece of the Scion is in St. Francis Folly of Greece.
Lara departs to Greece, and finds the second piece of the Scion in the depths of a tomb. While observing the empty coffin of Tihocan, the second member of the Triumvirate, Lara is told at gun point to give up her piece of the Scion by Pierre. After Pierre takes the piece Lara tries to take him by surprise but he escapes with the Scion piece in hand, only to be killed by guardian centaurs outside of the tomb. After defeating the centaurs, and assembling both pieces of the Scion, Lara has a vision that reveals the location of the third and final piece of the Scion: Egypt.Lara travels to Egypt, and successfully retrieves the third piece of the Scion. After assembling all three pieces, Lara’s earlier vision becomes much clearer. Two of the three Triumvirates, Tihocan and Qualopec, are sentencing the third one, revealed to be Natla, to banishment in Lara’s vision. Natla, after releasing Atlantis’ own army against itself in an attempt to bring about the Seventh Age, is imprisoned in the crystalline structure for a thousand yearsWith Lara in a trance from watching the vision, Natla steals the Scion, and has Lara restrained by her three henchmen. Lara escapes and follows the departing Natla on a motorbike, managing to sneak onto Natla’s departing boat. Lara follows Natla into a desolate mine, and kills Larson when he tries to stop her progression. Visibly shaken, Lara then confronts Kold and Kid, who end up killing each other in the skirmish. Lara then travels to the top of the Atlantean pyramid and confronts Natla.Not long into the confrontation with Natla, Lara realises that Natla’s plan is to resurrect the army of Atlantis. Natla attempts to convince Lara to stop opposing her, and become immortal like she is. Lara shoots the levitating Scion in response, and is then tackled by Natla, who falls into the molten liquid while Lara uses her grappling hook to survive. Lara, thinking Natla dead, tries to escape, confronted by a giant mutant along the way. She is soon confronted by an angry Natla, scorched in appearance, but unimpeded in ability. After a confrontation, Lara collapses a pillar supporting the pyramid onto Natla, trapping her under the collapsing pyramid. Lara escapes and sails away in Natla’s boat