In 1945 in New Mexico, a blast from a nuclear experiment during the Manhattan Project reveals a strange crystalline structure, from which a winged creature breaks free and flies away. In Calcutta (now Kolkata, India) 1996, Lara Croft is approached by Larson Conway, who introduces her to Jacqueline Natla, who wishes 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 the Atlantean king Qualopec. She discovers that he was one of three 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 and finds evidence that the next piece of the Scion is located in St. Francis Folly in Greece.
Lara departs to Greece, and finds the second piece of the Scion in the depths of a tomb. While Lara studies the empty coffin of Tihocan, the second member of the Triumvirate, Pierre ambushes Lara, forcing her at gun point to give up her piece of the Scion. 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 joining both pieces of the Scion, Lara sees a vision, and it 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. In Lara's visions two of the three Kings, Tihocan and Qualopec, are sentencing the third one, revealed to be Natla, to imprisonment. Natla, after releasing Atlantis' own army against itself in an attempt to bring about what she refers to as the Seventh Age, is imprisoned in the crystalline structure for a thousand years..
With Lara in a trance, 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. 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 her. Lara destroys the Scion instead, and is then tackled by Natla, who falls into the lava while Lara uses her grappling hook to survive. Lara, thinking Natla dead, tries to escape, being confronted by a giant mutant along the way. She is soon confronted by an angry Natla, severely burnt, 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.
The score for Tomb Raider: Anniversary is composed by Troels Brun Folmann. It took 5 months for Troels to compose, and is in the style of electronic orchestra. The majority of the album contains his original scores and themes. However, recognisable themes from the first game (composed by Nathan McCree) such as "Time to Run", "Puzzle Theme", and "Puzzle Theme II" have been recreated.
Folmann's work for Anniversary is different from that of Legend, as it has no underlying techno beats or electronic effects. Anniversary's score resembles that of a combination between the original Tomb Raider and a typical movie score: entirely orchestral and choral. Folmann uses more complex instrumentation and composition in his scoring, acquiring more woodwinds, instrument articulation, and ambience. Folmann leaves somewhat of a trademark in his Anniversary music by adding a significant amount of wind chimes throughout the score.