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Tomb Raider III opens millions of years ago, when a meteoroid survived the plunge through the Earth's atmosphere, impacting the then-warm climate of Antarctica. The first people to discover this land were a tribe of Polynesians. Despite the now-freezing conditions, there was an abnormal abundance of life and the tribe settled, worshipping the meteorite crater for the powers it appeared to hold and then forged parts of the meteorite into four artifacts. Generations later, though, catastrophic events forced them to flee in terror. Today, the same area is being excavated by the research company RX Tech, headed by the eccentric Scotsman Dr. Willard. The team is picking up unusual readings from the meteorite's impact zone. Soon after they uncover the body of a sailor from Charles Darwin's voyage on the Beagle. It seems a few of his sailors had explored the interior of the crater.
- Once again, Tomb Raider III pays homage to Indiana Jones in a number of ways, most notably by referencing The Temple of Doom in the India segment. In the South Pacific, certain traps can be triggered by walking into a beam of light just as in Raiders of the Lost Ark. In the secret room of her mansion, next to the artifacts of the previous games, Lara keeps a gold idol stored resembling the one Indiana Jones recovers in the introduction of Raiders of the Lost Ark.
- References to other popular movies include Jurassic Park, Independence Day, Batman, Mission: Impossible and The Fly.
- The model of Sophia Leigh is the same one used for Lara herself, but with a different hairstyle and other clothes.
- Some versions are censored, making Lara's blood pink instead of red.
- For most of the Antarctica levels, after the "Antarctica" level, Lara seems to be going down deep into the Earth until the "Meteorite Cavern" level.