Story

In 1945, a military testing in Los Alamos, New Mexico takes place, where a nuclear experiment during the Manhattan Project causes an unknown flying creature to be set free. In 1996, Lara Croft meets up with Larson in an Imperial hotel in Calcutta, India. He introduces her to his boss, Miss Jacqueline Natla. She suggests a job to Lara, to find a piece of the Scion in Peru. Lara is intrigued.

Lara and her guide are trekking in Peru. She opens up a doorway in the caves and wolves charge out, killing her guide. Lara kills them and ventures in. After some time, she comes across a piece of the Scion in the Tomb of Qualopec, one of three rulers of Atlantis before it sank. As she leaves, she notices the figure of Qualopec moving before the tomb collapses. She makes her escape and sees Larson waiting for her and the piece. They fight but Lara wins. Larson, at gunpoint, says that Natla has sent Pierre DuPont to find the second piece of the Scion. Lara knocks him out and steals his shotgun before leaving.   ​

She breaks into Natla's office and learns that Pierre and the next piece is located in St. Francis Folly in Greece, a place that she knows of.  

In Greece, Lara finds the second piece of the Scion in the Tomb of Tihocan, a second ruler of Atlantis. After opening the empty coffin of Tihocan, Pierre holds a gun to her head. They fight but he escapes with the Scion piece. This upsets the now living centaurs outside and Pierre realises this so he throws the Scion piece to Lara. The centaurs still kill Pierre DuPont for stealing the piece. After defeating the centaurs, Lara joins both pieces of the Scion and sees a vision, revealing the location of the third and final piece of the Scion in Egypt.   ​

Lara finds it in the Sanctuary of the Scion in Egypt when she connects all three pieces, she sees another vision - Tihocan and Qualopec are sentencing the third ruler, revealed to be Natla, to imprisonment. Natla had used the Scion's power and Atlantis' own army against itself to bring about the Seventh Age, but she is imprisoned in a crystalline structure for a thousand years.

Lara wakes from the vision and sees Natla in front of her, who has just stolen the Scion from her hands. Natla orders her henchmen to kill her but Lara escapes and follows the departing Natla on her motorbike, before managing to sneak onto Natla's yacht. Later, she sees a small boat making its way towards an island and Lara follows.

Deep in the abandoned mine, she meets up with Larson again. They fight once more but Lara kills him. She is upset for doing it as this was her first human kill but she pushes on, meeting Kold and Kid, who end up killing each other whilst trying to kill Lara. She traverses her way to the top of the Atlantean pyramid and confronts Natla.  ​

During the confrontation, Lara realises that Natla's intention is to resurrect the army of Atlantis. Natla attempts to convince Lara to stop opposing her, with the bribe of becoming immortal like her, but Lara destroys the Scion and is tackled off the ledge by Natla, who falls into the lava below whilst Lara uses her grappling hook to cling to safety. She believes that Natla is dead as she pulls herself up onto a ledge, but after she stands, the large egg clinging to the wall opposite begins to hatch. It is one of Natla's experiments, a giant mutant, and it tries to prevent Lara from progressing further. She manages to defeat it but is later faced by a mutated Natla. After a tough fight, Lara pulls a weak pillar onto her, trapping her in the collapsing pyramid. Lara escapes and sails away in Natla's yacht.