Archaeologist-adventurer Lara Croft is approached by a mercenary named Larson, who is working for businesswoman Jacqueline Natla. Natla hires Lara to acquire the Scion, a mysterious artefact buried in the tomb of Qualopec within the mountains of Peru. After recovering the Scion from Qualopec's tomb, Lara is confronted by Larson, who reveals that she is holding a piece of the artefact and Natla has sent rival treasure hunter Pierre Dupont to retrieve the other pieces. Breaking into Natla's offices to find out Pierre's whereabouts, Lara discovers a medieval monk's prayer book, revealing that the Scion was divided between the three rulers of Atlantis and that the next piece is buried beneath an ancient monastery of St. Francis' Folly in Greece.

Navigating the monastery, Lara finds the tomb of Atlantean ruler Tihocan, where she kills Pierre and recovers the second piece of the Scion. From a mural, she learns that Tihocan unsuccessfully tried to resurrect Atlantis after a catastrophe struck the original land. After joining both pieces of the Scion, Lara sees a vision that reveals the third and final piece of the Scion was hidden in Egypt after the third Atlantean ruler, a traitor who used the artefact to create a breed of monsters, was captured by Tihocan and Qualopec. Making her way through Egypt to the lost city of Khamoon, Lara kills Larson and recovers the third Scion piece.

Emerging from the caves, Lara is ambushed by Natla and her three henchmen, who take the Scion. Lara escapes and stows away aboard Natla's yacht, which takes her to an island holding an Atlantean pyramid filled with monsters. After dispatching Natla's henchmen and making her way through the pyramid, Lara finds the Scion and sees the rest of the vision, revealing Natla to be the betrayer. Lara faces Natla, who reveals that she intends to use her army to push forward humanity's evolution, as she believes both Atlantis and current civilisation are too soft to withstand disaster. Lara decides to destroy the Scion, and Natla's attempt to stop her sends her into a crevasse. After fighting a large legless monster, Lara shoots the Scion, setting off a chain reaction that begins to destroy the pyramid. Lara kills a winged Natla and escapes the exploding island.