Lara Croft (Keeley Hawes) heads into Bolivia on a tip from Anaya to find a stone dais in the ruined city of Tiwanaku. Lara believes the stone is connected to her mother's disappearance following the plane crash. A flashback shows young Lara activating a similar dais in a Nepalese monastery, creating a magical portal; Amelia vanishes upon drawing an ornate sword from the dais after hearing voices from the portal. Fighting through mercenaries exploring Tiwanaku, Lara confronts their employer, James Rutland, who has a fragment of a sword identical to the one from Nepal. Before leaving, he mentions Amanda Evert (Kath Soucie) as if she were still alive. Lara meets with Anaya in Peru near the site where Amanda died. In a flashback, Lara and Amanda are seen as part of an archeological team investigating a buried tomb. A powerful "Entity" guarding the tomb killed everyone but them before vanishing when Amanda pulled a stone from a door to open it. The tomb flooded, and Lara was forced to abandon Amanda after she was seemingly crushed by falling debris.
Lara drains the flooded tomb and proves that Amanda survived and is now working with Rutland to find the sword. At the tomb's heart, Lara finds a statue of Tiwanaku's last queen whose life strongly parallels the common legends of King Arthur and a replica of her sword. The tip resembles an artifact stolen by Takamoto from Waseda University. In Tokyo, Lara's negotiations with Takamoto break down, and she storms his offices before facing and defeating him in a final duel. The stolen sword fragment, which has destructive magical abilities, was discovered by an 11th-century crusader said to have been a knight of Arthur. Lara then pursues Rutland to a Ghanaian temple hidden behind a waterfall that Richard Croft explored during his career. Rutland is searching for the Ghalali Key, a talisman which can reforge the sword. During her explorations, Lara finds a pendant belonging to Amelia. Confronting Rutland, who assumed Richard found the Ghalali Key, Lara takes his sword fragment, having learned that Amanda has ransacked her home in search of it.
Lara pursues Amanda to Kazakhstan, where she discovers a 1950s-era Soviet research base that unsuccessfully tried to weaponise the sword's energies. Amanda, now bitter about the events in Peru, races her to the artifact. She eventually unleashes the tamed Entity on Lara using its control stone. Lara avoids the Entity and retrieves the sword fragment as the ancient facility disintegrates. Lara also discovers the shield of the knight who had the fragment, bearing an ancient map. The decoded map leads Lara to Cornwall and a King Arthur-themed tourist museum built over a hidden complex housing the tombs of King Arthur and his knights around a broken dais. She realises that the sword she is pursuing is the legendary Excalibur one of many swords forged by an unnamed civilisation that have created a monomyth within multiple later cultures left in pieces and scattered across the world by Arthur's knights.
Retrieving the fragment left with Arthur, she escapes the tomb and the sea serpent protecting the sword. Back home, the group realise that the Ghalali Key was found in Ghana by Richard and given to Amelia to replace the pendant she lost; it now lies with the crashed plane in Nepal. During a talk with Winston, Lara reveals her determination to salvage her father's ruined reputation by using Excalibur to prove his theories about the daises. Returning to Nepal, Lara recovers the Ghalali Key, then travels to the monastery holding the original dais and reforges Excalibur. The broken dais splinters when she tries to use it, forcing her to return to the intact dais in Bolivia. On reaching it she is forced to kill Rutland during a fight with his mercenaries and destroys the Entity when Amanda summons and merges with it. Placing the sword in the dais, Lara activates a portal and sees a vision of Amelia. Realising that the portal is a time rift, Lara tries to warn Amelia, but Amanda panics and shouts to remove the sword before the dais explodes, triggering the events of Amelia's apparent death. An enraged Lara almost shoots Amanda, but Amanda says that Amelia was transported to Avalon. Lara knocks Amanda unconscious and sets out to find Amelia.