Atlantean Pyramid
At the top, it contained the cryo-genic freezing device that was used to freeze Natla as her punishment. Inside the pyramid, there were vast corridors and great rooms, constructed of stone and muscle tissue. The centre of the pyramid contained the largest room which spanned from the bottom of the pyramid to the top. At the top of this great room, lay the device where the Scion was to be placed. The bottom was filled with lava. Throughout the pyramid, there were hatcheries that Natla used to create her mutant army. The Master Mutant was hatched on a large platform in the great central room.
The pyramid was the only surviving building after Atlantis was destroyed. Over the years it was eventually covered up in mud and rock, and it became an island, with its entrance being submerged underground.
Natla having escaped, reactivated the pyramid using the Scion which she took off Lara. The mud and rock surrounding the pyramid crumbled, and it gleamed in the sun once more. When the Scion was destroyed by Lara, the power of the pyramid became unstable, and it exploded with a violent outburst. Lara escaped in time.