The plot opens with a flashback sequence showing a nine year old Lara Croft traveling with her mother. The plane carrying them crashes into the Himalayas, apparently leaving them as the only two survivors. After taking shelter in the ruins of an ancient temple, Lara discovers an ornate stone dais holding a sword whilst searching for firewood. She unwittingly activates the ancient artefact and watches in horror as her mother vanishes in front of her eyes into a portal.

Years after the plane crash, Lara, now an adult, travels to Bolivia after one of her friends, Anaya Imanu, mentions a stone dais located in the ruins of Tiwanaku, a pre-Incan civilisation. After following a twisting rocky path, she runs into a group of mercenaries who are under orders to attack her on sight. After disposing of them, she proceeds to a temple encountering more mercenaries and dangerous native wildlife along the way. On the other side of the temple, she sees the dais and finds James Rutland, an American socialite and self-proclaimed adventurer. Rutland mentions Amanda Evert, a friend of Lara's who supposedly died years before, and then orders his mercenaries to kill Lara. She overcomes them and reaches the dais, confirming that it was the same as the Himalayan one.

Lara meets Anaya at a village in Peru, and after another battle with Rutland's mercenaries, they reach the tomb in Paraíso, where a tragedy befell them years ago. A flashback sequence shows Lara on an archaeological excavation with her university colleagues, where she and Amanda witness an unknown entity kill the rest of the team. The entity vanishes when Amanda removes a mysterious glowing stone from a wall, but this also causes a cave-in that floods the cavern. Amanda becomes trapped under a pile of rubble, leaving Lara with no choice but to escape or drown: she flees the cavern, seemingly leaving Amanda to her death.

Back in the present, Lara discovers the artefact she is seeking may be linked to Excalibur -- part of the King Arthur legends -- and that Amanda survived the cave-in and is looking for the sword, which reportedly had been broken into four fragments which are now spread across the globe. Lara, now realising what she is looking for, recalls that one piece is in the 'care' of Yakuza boss Shogo Takamoto, who had it stolen from Waseda University. Lara travels to Japan, where her friend in the Japanese media, Toru Nishimura, assists her in setting up a meeting to negotiate with Takamoto for his fragment. Takamoto refuses to negotiate, claims he has no idea what she is talking about, and orders his goons to kill Lara. Lara dispatches the goons and chases Takamoto across the rooftops of Tokyo all the way to the roof of his penthouse apartment. Takamoto uses the power of the fragment to attack Lara but she kills him and recovers it.

Lara proceeds to Ghana, to a temple site her parents worked on before she was born, where she finds Rutland again, who is also in possession of a sword fragment. She follows him into an ancient temple hidden behind a waterfall. When she reaches Rutland, he mentions an artefact called the Ghalali Key, believing that Lara's father found it and it is now in Lara's possession. Lara appears to have no knowledge of the key and this frustrates him. Rutland then attacks her using his sword fragment but Lara subdues him and grabs the second fragment. She then receives news from Zip and Alister that Amanda raided Croft Manor looking for the Ghalali Key only moments ago. She offers to return to the Manor to see if they are alright, but they persuade her to try and beat Amanda to Kazakhstan, the apparent location of the third fragment.

When Lara arrives in Kazakhstan, she discovers that Rutland's men have taken over a Soviet lab where experiments on a sword fragment were conducted by the KGB fifty years ago. Lara catches up with Amanda, who is still bitter about being left to die in Paraíso. Lara goes after her and finds her conducting experiments on the third sword fragment. Amanda is also using the glowing stone she pulled out of the wall in Paraíso to control the unknown entity that attacked them. Lara avoids the entity since it can not be defeated yet, while she recovers the third sword fragment.

Following a map on the back of a shield (supposedly Lancelot's) also found in the Soviet lab, Lara's search brings her home to England. She discovers the real King Arthur's tomb hidden under a tacky and now-derelict King Arthur tourist attraction in Cornwall, along with the final sword fragment. Inside the tomb, Lara discovers that after Arthur's death, four of his knights - Lancelot, Percival, Galahad and Bors- took fragments of the sword to locations around the world (inspiring the myth of the Grail Quest), while the final fragment was left with Arthur by Bedivere in the hope of resurrecting the Once and Future King. After slaying a giant sea serpent that guards the tomb, and a group of mercenaries that have followed her, Lara returns to Croft Manor to figure out how to put the four sword fragments back together.

Lara realizes that the Ghalali Key was in fact a pendant given by her father to her mother, and that her mother had it with her when their plane crashed in the Himalayas. Lara returns to the crash site in Nepal to find the Ghalali Key (it had been in her mother's possession, given by her father to replace a locket she lost on the Ghana expedition, which Lara actually finds on her own excursion in Ghana). After traversing high ledges to reach the ruins of the plane, she finds the key in the wreckage, then narrowly escapes as the plane topples over the edge of a cliff. Lara then proceeds, emotionally shaken, to the temple she and her mother found after the crash. She runs into Rutland's mercenaries, quickly defeats them and enters the temple to restore Excalibur. She wonders if the dais is still active, but it merely collapses when she places the sword in the stone.

Lara returns to the stone dais in Bolivia, where Amanda, Rutland and their mercenaries await. Lara uses Excalibur to kill the mercenaries and inadvertently kills Rutland as well. Amanda rushes over to him, and he dies in her arms. Lara apologises and tries to patch up the rift with Amanda, suggesting they use the sword together. Amanda angrily refuses and releases the entity again, this time merging with it to become more powerful. With the power of Excalibur, Lara defeats the entity and separates it from Amanda, destroying it this time.

Lara uses Excalibur on the dais to reopen the portal and discovers what happened to her mother. Lara realizes that the portal spans time and she is seeing her mother moments before she disappears. Amanda gets up and shouts at Lara to pull out the sword or the dais will explode. Lara's mother hears this through the portal, pulls out the sword, and the dais explodes. Amanda berates Lara for her actions: however, Lara is unconcerned, furious at the realisation that Amanda was responsible for the apparent causality loop that claimed Lara's mother.

Lara fires a hail of bullets around Amanda and places her gun to Amanda's head, threatening to kill her if she doesn't explain. Amanda states that Lara's mother isn't dead, but in Avalon, where Amanda herself wanted to go. She hisses that she is wasting her breath, that Lara will never understand. Lara spares Amanda's life, but settles for knocking Amanda out with her pistol, snarling that "From this moment, your every breath is a gift from me". The game ends as Lara, determined to find answers, tells Zip and Alister they still have much work ahead of them.

In 1945 in New Mexico, a bomb explodes, engulfing a town and revealing a strange 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 artefact called the Scion, located in the Peruvian mountains. Lara, having searched unsuccessfully for such an artefact with her father in the past, agrees to go.

In the Peruvian mountains, Lara finds a tomb belonging to a 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 Greece.

Lara departs to Greece, and finds the second piece of 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 a crystalline structure for a thousand years.

With 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.

The story begins with Lara Croft in the lower corridor of Croft Manor where Lara has to escape from a fire. Upon entering the main hall, she is surprised to see the mansion in flames. As she reaches the main door, Zip shoots at her as Winston tries to restrain him. The game flashes back a week into the past, showing Lara in the Mediterranean Sea.

Mediterranean Sea

In the Mediterranean Sea, Lara is searching for a way to Avalon, the mythical resting place of King Arthur, and the place where Amanda claimed Lara's mother is. Lara finds a temple of "Proto-Norse" origin, leading her to believe that Avalon and the Norse underworld of Niflheim are one and the same. Inside Niflheim, she defeats a Kraken, and finds one of the Norse god Thor's gauntlets. Lara is attacked by mercenaries working for Amanda, who take the gauntlet to Amanda's ship, and leave Lara trapped. Lara escapes and makes her way onto their ship, where she encounters her old nemesis, the former ruler of Atlantis, Jacqueline Natla, whom Amanda has in captivity. Natla informs Lara that Avalon is not Niflheim, but rather a different location called Helheim, and that Lara will need Thor's hammer, Mjölnir to enter it. Natla suggests that Lara should pursue her search in Thailand. Amanda's ship suddenly begins to sink because of an explosion caused by Lara's firefight against the mercenaries. Amanda escapes by helicopter, taking Natla with her, and throws the gauntlet into the sea, because Natla told her that it would only work for Lara. Lara quickly dives after it and catches it.

Coastal Thailand

Lara then travels to coastal Thailand, where she finds ruins associated with Bhogavati and guarded by ravenous naga. Where the second gauntlet should be, Lara instead discovers that her father had already been there and had taken the second gauntlet back to a hidden study beneath Croft Manor, also obliterating a map on the gauntlet's pedestal.

Croft Manor

Lara then returns to Croft Manor, her home in England. With the help of Zip and Alister, she discovers a secret passage to the crypts under the manor. Lara makes her way through the underground passageways and retrieves the gauntlet, and finds a photograph of the destroyed map from Thailand, taken by her father, which shows the separate locations of Thor's belt and hammer.

When Lara makes her way back up to ground level, the game's introductory scene is repeated; She is surprised to find the manor going up in flames. As she reaches the main door, Zip shoots at her as Winston tries to restrain him. They exit the manor, and Zip explains that he saw Lara shoot at him after taking Amanda's "Wraith Stone" from Lara's own vault. Lara and Winston convince Zip that it was not Lara, but rather an impostor. She goes back inside to view the security video in the computer room, but before she has a chance to do so, she is attacked by her doppelgänger. The doppelgänger subdues Lara, shoots and kills Alister, who was trying to escape the flames, and then flees. Lara carries Alister's body out of the house, and resolves to continue searching for Mjölnir, which she believes will give her the power to kill Natla.

Southern Mexico

In Mexico, Lara discovers ruins leading to a subterranean area identified as Xibalba. Inside, she retrieves Thor's belt, which powers the gauntlets needed to wield his hammer.

Jan Mayen Island

After retrieving the belt, she heads to Jan Mayen Island and finally finds Mjölnir deep in the ancient stone halls of Valhalla. She also finds a message from Odin, Thor's father, which states a certain ritual must be performed in order to open Helheim's entrance.

Andaman Sea and Arctic Ocean

Now armed with Thor's gauntlets, belt and hammer, Lara confronts Natla on Amanda's second ship, in the Andaman Sea. Lara reluctantly agrees to work with Natla, who claims to know Odin's ritual, and sets her free from Amanda. Natla gives Lara the coordinates to Helheim, in the Arctic Ocean.

There, Lara finds her way to the underwater ruins surrounding Helheim, and, with Natla's help, opens the entrance. She soon encounters her mother, Amelia, who has been turned into a thrall, a deceased individual whose corpse is reanimated by the substance eitr. As the mindless thrall approaches, Lara forces her back into the eitr. Lara kneels in sorrow as Natla appears to reveal that she was using Lara and Amanda to gain access to Avalon, via Thor's hammer. Natla also reveals that she killed Lara's father, Richard, when he refused to cooperate in this task years ago. The doppelgänger appears and restrains Lara just as she was about to attack Natla with Mjölnir. As Lara is about to be killed, Amanda appears and uses her Wraith Stone to throw the doppelgänger over the precipice, apparently into the eitr. She also holds off the approaching thralls, allowing Lara to pursue Natla.

Lara finds Natla activating a massive, ancient device at the heart of a titanic cavern filled with eitr. Natla explains that Jörmungandr, the Midgard Serpent, refers to the network of tectonic divisions spread across the world beneath the oceans giving rise to the legendary interpretation of the creature encircling the world. Natla explains that this device sits right atop where the supercontinent, Pangea, had split apart millions of years ago, and once activated, is designed to bring about Ragnarök, or what Natla refers to as the Seventh Age, by triggering apocalyptic levels of volcanic activity throughout the world.

Lara destroys the device with Mjölnir then hurls the hammer at Natla, who is distracted by trying to repair the machine. Natla is struck down and plunges into the eitr. Lara heads back to Amanda, but they discover that the exit is blocked. Lara spots the portal that originally brought her mother to Helheim, realizing that her mother may not have known how the device had worked thus remaining trapped. Lara and Amanda work together and escape.

They are teleported back to Nepal, where Lara's mother accidentally teleported herself to Helheim. Amanda attempts to stir up a fight with Lara, who chastises her. Amanda contemplates her choices, before finally limping away. Alone, Lara mournfully bids goodbye to her mother, and the game ends as she walks away from the portal.