Well, Tomb Raider VI was about this mysterious race of near Immortals (they could be killed, but it wasn't easy, you either had to cut off all their limbs and head or shatter all their bones) who used Alchemy to do a variation of genetic engineering.
In addition, their eldest members had special powers, which made fighting them even harder.
Mind you, Lara naturally saw that as a challenge, plus she had the Periapt Shards (daggers that could kill them).
Actually, the Shards could kill anything if it was evil.
And since this race weren't walking on the nice side of the fence, they were particularly vulnerable to the Shards.
I'm assuming the second part of that story would have dealt with the awakened Sleeper (he was the most powerful member of that race) and bringing him down.
Lara awakes the Sleeper at the end of the game, but what happens afterwards, we never found out.
It would be very strange to have a being that powerful wake up and then just fade away into obscurity.
The third part of the story, well, I'll don't know how that was going to be played out.