Millions of years ago, a meteorite strikes Antarctica, decimating a large area full of life on the then-near-tropical continent. In the present day, a corporation called RX Tech, under the guidance of Dr. Mark Willard, excavates the site, finding strange Rapa Nui-like statues and the grave of one of HMS Beagle's sailors. Within the game, while India must be visited first and Antarctica last, the three other locations: South Pacific Islands, London, and Nevada, can be visited in any order. When the game begins, Lara Croft is searching for an artifact known as the Infada Stone in the ruins of an ancient Indian Hindu temple once inhabited by the Infada tribe.
She encounters a researcher working for RX Tech who appears to be insane. After parting ways, the researcher beats Lara to the Infada Stone, gaining supernatural powers. After killing him and taking the artefact, Lara is approached by Dr. Willard, the head of RX Tech, who explains the origins of the Infada Stone. Thousands of years ago, Polynesians came across the meteorite crater and found that it had incredible power. Using rock from the meteoroid, they crafted four crystalline artifacts, one of which is the Infada Stone. They then fled Antarctica for unknown reasons, but, in the nineteenth century, a group of sailors travelling with Charles Darwin came to Antarctica and discovered the artifacts. The four stones were then distributed across the globe. Dr. Willard has been able to track the artifacts by using the diary of one of the sailors. Lara agrees to help find the other three stones. On an island in the South Pacific, Lara fights cannibal tribesman, Velociraptors, a T-Rex and encounters a wounded soldier who tells her of a deity who lives in the hills of the island.
Lara pursues the deity and learns from one of the tribesman that one of Darwin's sailors brought one of the artifacts to the island from Antarctica. She also learns about why the inhabitants fled their city there; the son of the leader was born without a face, caused by prolonged exposure to the Meteorite. Lara then infiltrates the deity's temple and defeats the deity Puna, who has immense power granted by the meteor artifact called the Ora Dagger. In London, Lara searches for the Eye of Isis, now in the possession of Sophia Leigh, the head of a cosmetics corporation. Lara learns that the corporation has performed sick experiments on humans in order to achieve immortality and eternal youth for Sophia's personal gain. The deformed subjects of Sophia's failed experiments, presumed dead by the corporation, were dumped in the sewers, and assist Lara in exchange for a bottle of embalming fluid from the Natural History Museum. Sophia sends a number of assassins to kill Lara, but they are all unsuccessful and Lara climbs through a ventilation shaft to Sophia's office where she is sitting with the artifact on her desk. Sophia mockingly offers Lara a job, telling her that with her lifestyle she would be the perfect face for her products, then Lara tells Sophia that her human subjects she experimented on are still alive.
Lara demands she hand over the artifact which she refuses to do. Sophia takes the artifact and runs out the balcony to the other building and Lara who works her way up Sophia's building and across to the one she is on. Sophia attempts to kill her using the powers of the artifact, but Lara defeats her by shooting a fuse box connected to an electric bridge that Sophia is standing on, electrocuting her. Arriving in Nevada and making her way through a desert canyon, Lara tries to enter Area 51, where Element 115, one of the four artifacts, is located in an alien spacecraft guarded by the government. But she faces a severe setback when she is taken as a prisoner in the base after her attempted break-in ends disastrously. Freeing herself and the other inmates, she escapes the security compound and stows away in a truck to Area 51.
Once she gets to Area 51, she eventually stows across a guarded spaceship that houses aliens, and eventually grabs the artifact from the main room. Lara then travels to Antarctica and discovers that Dr. Willard had been using the knowledge gained from the meteor to perform experiments on his own men, turning them into horrible mutations. Angered by this revelation, she confronts Dr. Willard, who reveals that he is planning to encourage rather than halt the mutations, only on a global scale, using the combined power of the artifacts and the meteorite they were carved from. As Lara voices her opposition to his operation, Willard betrays her, stealing the artifacts and disappearing into the excavation site. After fighting more mutants (including insectoid and reptilian life forms within the city itself) and navigating the treacherous ruins of the ancient city built atop the meteor crater, Lara faces Willard, who has now used the power of the four artifacts to activate the even greater power of the meteor: to greatly speed up the evolutionary processes of the human body and thereby turning himself into a terrifying spider-like creature. Lara deactivates the meteor by taking the artifacts out of their positions that they were put in, kills the mutated Willard and escapes by helicopter.
Tomb Raider III sees fictional archaeologist, Lara Croft, return as the game's main protagonist and only playable character. The game features several antagonists, notably Dr. Willard, who first hires Lara to retrieve four artifacts but reveals at the end of the game his more sinister motives. The South Pacific levels features Puna, an islander posing as a deity with the power of an artifact. In London, Lara is confronted by Sophia Leigh, a ruthless business woman who owns a cosmetic company which is experimenting on its employees in order to achieve the secret of immortality. She is in possession of one of the meteorite pieces. The game also marks the second appearance of Lara's butler, Winston, who appears in the Croft Manor training level as he did in Tomb Raider II.
Tomb Raider III: The Lost Artifact is a mini-sequel to Tomb Raider III, sometimes unofficially called Tomb Raider III Gold. It was released exclusively for PC in 2000 and later on Mac OS in the Tomb Raider Trilogy by Aspyr. Unlike the expansion packs for the first two games, this was initially sold as a standalone product rather than as part of a re-release, and was not available for free download for existing owners. It was released alongside the original game in the Premier Collection. In The Lost Artifact, Lara learns of the existence of a fifth meteorite piece called the Hand of Rathmore. She begins her investigations at the castle of Dr. Willard in the Scottish Highlands, progresses to exploring the Channel Tunnel in Dover and then ultimately ends up in the Catacombs of Paris, where she is again confronted by Sophia Leigh.