Amanda saves Lara from the doppleganger and they blast her into that blue watery-stuff below. Only she didn't hit the water and hit the ground instead. So she wakes up and you have to go through a modified version of part of the last Underworld stage. She finds Natla still alive, but badly injured. Natla commands her to bring her back to the doppleganger's "birth place," which is just another similar area filled with the deadly water-stuff (and of course, lots of thralls). There's an ancient machine there that can create and heal life, so Natla commands the doppleganger to go and "fix" the machine. After that, she returns to Natla, who tells her to go and kill Lara, then off herself since Natla never wants to see Lara again. This pisses the doppleganger off, but she has to follow orders.

It then shifts to the end cut scene from Beneath The Ashes, but with modified dialogue. Lara talks to the doppleganger and ends up giving her freedom from being under anyone's control (WTF, she killed Allister!), and then the doppleganger returns to Natla to kill her instead. Natla is inside a pod that is beginning to heal her, and the doppleganger can't get to her unless she stops the machine. (So you have to go back through the same area as before, only harder,
and thankfully filled with enough new platforming sections that it doesn't feel too tedious, stop the energy from feeding into the machine, and destroy the "circuits" inside.) After the doppleganger stops the machine, she returns to the pod room and takes out the two circuits inside there, toppling the pod and Natla with it.
Natla is trapped under a bunch of rubble, slowly melting into a pool of energy-water beneath her. She demands that the doppleganger help, but the doppleganger just stands there with this twisted smile, watching Natla melt into nothingness. The end.
So the doppleganger is still alive. Amanda too. Will they return in another game?