The simulation is so perfect that people only realize it is fake by attempting to generate random numbers; since computer code is pseudo-random, everyone in the simulation produces the same sequence.

Upon realizing he is a "simulacrum," the virtual Doctor uses his sonic sunglasses to record the entire experience and emails it to the real Doctor in the physical world as a warning of the impending invasion. The Vault & Missy

The episode's central mystery involves the , an ancient text in the Vatican's secret library that causes anyone who reads it to commit suicide.

A series of flashbacks explains how the Doctor ended up guarding the mysterious vault under St. Luke's University: Doctor Who S10E6: Extremis - FilmInk