Lara wakes up sometime later to find that they have arrived at their destination: a deserted island in the middle of the ocean. Lara enters through a coastal cave and discovers Natla's mines, a series of caverns that have been under extensive mining operations. Lara eventually retrieves her pistols from a small hut and defeats the cowboy upon encountering him. She retrieves her magnums and later the Uzis after defeating the skateboarder. She finally defeats the large man outside the excavated entrance to the Great Pyramid of Atlantis, hidden beneath the mountain. After retrieving her shotgun, Lara opens the pyramid doors and enters just as Natla places the completed Scion on a pedestal at the top of the pyramid, restoring power to the entire building.
Inside the pyramid, Lara finds the walls covered in pulsating flesh and pods that when hatched release the same mutants she had seen in her vision. Despite daunting odds, Lara makes her way up the pyramid, mostly by ascending the center chamber, an impossibly tall shaft with a pit of lava at the bottom. Along the way, Lara encounters a skinless doppelganger of herself that copies her every move, but manages to trick it into falling into a pit of lava. She also finds herself in a throne room at one point, with two thrones depictiong the letters T and Q respectively, representing Tihocan and Qualopec, as well as a third throne bearing the letter N.Against all odds, Lara reaches the top of the shaft where the Scion is kept. Upon attempting to remove it, Lara receives another vision. In the vision, it is revealed that Natla is the third ruler of Atlantis. Thousands of years ago, she had betrayed her co-rulers by using the Scion for genetic experimentation in order to create an army of mutants. As punishment for her crimes, Natla had her piece of the Scion confiscated and she was imprisoned in a cryogenic device. She remained trapped in that device up until the nuclear test in the prologue.After the vision ends, Lara is greeted by Natla herself. Natla casually reveals that she plans to finish what she had started and create an army of even more powerful mutants, the first of which is gestating in a large pod on the far side of the shaft. Deciding that the only way to stop Natla would be to destroy the Scion, Lara aimed her pistols, only for Natla to tackle her in a panic and send them both falling into the shaft. Lara manages to save herself while Natla falls to her apparent death, just as the pod hatches and releases a massive mutant that has no legs and so drags itself around on its torso. Lara defeats it and makes her way back to the top of the shaft, where she fires at the Scion and destroys it.The Scion's destruction causes a chain reaction that threatens to destroy the pyramid and Lara has to quickly make her way through collapsing chambers filled with lava. As she nears the exit, she enounters Natla, now showing her true form as an Altantean and sporting functional wings and the ability to throw fireballs. Lara kills her for good and escapes the exploding island on Natla's yacht.