Dr Mark Willard is working in Antarctica when he comes across meteorite rock, the Meteorite Cavern and the grave of Paul Caulfield.
Meanwhile, Lara is in a Jungle in India, searching for a meteorite artefact. She encounters a man called Tony who talks of two guys called Randy and Rory in a nearby temple. She later sees Tony again, rafting down the River Ganges. In his chest he is wearing the Infada Stone. As Lara attempts to shoot him, he laughs and causes the ground to shake. The temple collapses and she dodges falling pillars. She decides to chase after him and makes her way to the Caves of Kaliya to fight him. After killing him, she takes the Infada Stone.
On her way back to the river, a small boat pulls up alongside it. It is Dr Willard and he beckons Lara on board. He tells her that there is more than one meteorite artefact and that he is looking for them. He passes her the journal of Stephen Barr, a sailor who travelled on the HMS Beagle when they stumbled upon the artefacts as well as the Meteorite Cavern. He hires her to find the other three, each one in Nevada, London and South Pacific. When Lara arrives in Nevada, she manages to become imprisoned in a military prison. She manages to escape and comes across an alien spaceship. Onboard is Element 115. She picks it up and leaves for her next location.
In the South Pacific, Lara works her way through a village and climbs into a hut where a soldier is resting - his plane had crashed and he had been injured. When Lara asks about crossing the swamp, he passes her a map and tells her that if she sees any of his men that she should warn them away from that place. She later finds the crash site and uses the rocket launcher on the plane to kill the raptors. With the area safe, she enters the temple; there is a tribesman there who tells her that he is fasting. When she points to the wall mural and asks him why his ancestors fled from Antarctica so suddenly, he tells her that their sixth leader Mauki was born without a face. People were afraid of him and ran away. He called Antarctica Koma Koma. Lara mentioned that they still worshipped him and he says that a white man later came to the South Pacific with a magic Koma Koma stone and people decided to celebrate the date of his death. Lara says that the man was one of Darwin's sailors. She asks the tribesman where the stone is but he doesn't answer her. Lara passes through Madubu Gorge to the Temple of Puna where she encounters a man called Puna, sitting on his throne. She manages to kill him and picks up the Ora Dagger that he had been using against her.
In London, Lara passes through Thames Wharf and meets a man on top of a Cathedral, who says that he works for a woman called Sophia Leigh. He says that his father and grandfather worked for her too. When Lara asks for her age, he guesses at late 20s or early 30s. As he attempts to threaten Lara, he gets hit by the swinging bell, knocking him over the roof top. Lara jumps through the hole in the roof to explore Aldwych station, only to later fall through another hole. When she looks up, a man drags her to his leader. The leader, wearing a mask, guesses that she is looking for Miss Leigh but not for revenge as she hasn't got the face for it. When she asks about his face, he says that he hasn't got a face. He tells her that he was once a lab assistant and due to a failed experiment, he and a few others lost their faces but had also gained immortality. He tells her that Sophia is after everlasting beauty, and that he is willing to help Lara if she helps them first. He wants Lara to collect a bottle of embalming fluid from the natural history museum. She agrees and works her way through Lud's gate, popping off momentarily to collect the embalming fluid. She returns back to their den and drops off the bottle, before making her way to Sophia's office. She spots that her next artefact has been slotted into a sceptre, and when Lara tries to grab the sceptre from the desk, Sophia takes it and heads outside. After a short fight, Lara kills Sophia and picks up the Eye of Isis.