Lara is contacted by her good friend, Professor Igor Bowmane, who works in the Ancient Artefact department at the University of Moscow. He told her of an old manuscript which recounts the last few years of the reign of Moctezuma II, found by a captain under the leadership of the Spanish Conquistador Cortez. The manuscript tells of the legend of the 'Nightmare Stone', and says that there was once an evil god called Quaxet, who ruled the Aztec, Mayan and Inca lands. To stop him, all three cultures joined together. Three High Priests defeated him, entombing his spirit into a crystal orb - the 'Nightmare Stone'. To prevent anyone from releasing Quaxet, the stone was sealed in an Obelisk and then sealed in a temple built by the Priests. Professor Bowmane tells Lara that his friend Illiat, a fellow curator in Peru, has warned him of 'interested parties' looking for the manuscript. Illiat has told them nothing and Bowmane wants Lara to find the stone before they do.
She sets off for Peru to meet Illiat; however he isn't where he said he would be. She finds his glasses and footprints leading into the temple. She finds a way inside to begin her search. Inside the temple, Lara soon finds a large altar. She touches the crystal front and is zapped with an energy, rendering her unconscious. She wakes up some time later to see the room is now brighter, but also a trail of blood. Lara decides to follow it.
She later finds an injured Illiat inside the first part of the Royal Tombs, pinned in by a mummy. She defeats it and kneels besides Illiat. He tells her that he has lost too much blood and is dying. When she asks him about what is happening, he asks her if she touched the altar and when she says that she did, he tells her that she has unleashed the guardians, spirits of the ancient protectors of the temple. They were entombed to make sure that the stone remained inside the temple. He refuses her help to leave and tells her to stop the mercenaries who want the map to the Nightmare Stone. They had captured him and tortured him, forcing him to show them what to do at the altar before they found the map and left him. He adds that he had tricked them and they had only made off with part of the map. Illiat says that they cannot get all the way down to the snake guardian, who holds the final part of the key that will unlock the Nightmare Stone. He gives her a map and tells her to go back to the altar and destroy the stone. He dies and Lara heads onwards.
Inside the Treasure Chambers, Lara finds a gold hunter, and she asks him about how to get into the lower chambers. He informs her about a room with sun and moon statues and that Lara will need amulets to put into the statues. Lara tells him that the curse has awoken the guardians and that he must go.
When she has made it through the Caverns and Volcanic Temple, Lara comes across Jaual Teotl, a snake guardian. After defeating it, she finds that it was guarding a crystal. She picks it up and races back to the altar. She places some panels she had discovered on her adventure into the front of the altar and a compartment opens up, revealing the Nightmare Stone. She realises that it must be destroyed, so she drops it into a lava pool. However, this causes the temple to begin collapsing and when Lara turns to leave, the exit is blocked. Quickly though, she finds a different route, and makes it outside. Lava bursts out through the temple and spills out into the surrounding land. Lara takes a moment to pause and look at a green crystal she had picked up, before leaving.