This starts out like a cross between Doctor Who and the Da Vinci Code. This business of an ancient text that contains some horrific secret has been the making of a thousand crappy novels, and I don't really like it much better, here. To my mind, we're faced with the paradox that people advanced enough and powerful enough to run a simulation of all of human history wouldn't need to do so.
I did like the bits with Bill's virtual and then real dates, however. That was pretty funny stuff.
Also: It's Missy in the Vault? That was the first guess I had, which I rejected as too obvious.
Overall: Not that amazing. More Moffatian contrivance.