The Doctor and Nardole

After the events in the previous story aboard the space station (see "Oxygen") The Doctor is still blind and is wearing his sonic sunglasses to provide limited sight while masking his condition from Bill Potts. While visiting the vault under the university he receives an email entitled Extremis that he views through his glasses.

In one of the university lecture halls The Doctor is visited by the Pope and members of the Vatican to help deal with a recently-translated text called Veritas, that causes readers to commit suicide.

The Doctor takes Bill and Nardole to the Haereticum - a secret library inside the Vatican. There they discover a priest who has just read the book and emailed a copy to CERN. He then flees and kills himself.

Bill Potts

While The Doctor is preoccupied, with the priest and the book, Bill and Nardole discover a portal leading to a hub containing other portals. One of the portals is seemingly linked to CERN while another is linked to the Pentagon and another to the White House. Meanwhile, The Doctor, having tried to read the Veritas, is forced to flee into a second portal with the priest's laptop when a skeletal figure in red robes, appear.

Bill and Nardole having entered the CERN portal, find the scientists are preparing to kill themselves using explosives strapped under the desks. When Bill asks why they are doing this the lead scientist, Nicholas, tells them that they are saving the world. When asked how, he replies that this is not the real world. Nicholas then asks Bill and Nardole to both pick a random number and say it at the same time. Each time they try they both say the same number. Nicholas tells them that this is a ‘Shadow Test’ proving that they are not in the real world.

The Pope

With seconds to spare Bill and Nardole manage to flee back to the hub. Nardole then realises that the projectors are actually projecting the locations. To his horror, he realises that the world is really a holographic simulation. To prove if he is correct he steps into the space between projections causing him to dissolve into pixels leaving Bill alone in the hub.

A distraught Bill then spots a trail of blood on the floor leading to one of the portals. She follows the trail and finds herself in the Oval Office of the White House, where The Doctor is waiting.

The Doctor explains to her that Veritas describes a ‘demon’ planning to invade Earth by creating highly detailed simulations to practice their invasion. He also reveals that the simulacra within these ‘shadow worlds’ are able to discover the false reality as they can only come up with pseudo-random numbers due to the nature of computers, leading them to commit suicide to escape the simulation.

The Doctor and Cardinal Angelo

A Monk then appears and Bill disintegrates the same way Nardole did. The Doctor, aware he is also a simulation, tells the alien that Earth will now be ready as he has been recording everything through his sonic glasses. He emails the recording, titled Extremis, to his real-world self who receives it when visiting the vault.

Throughout these events in the shadow worlds, flashbacks show The Doctor being summoned to perform the execution of Missy. The Doctor however, opted to spare her. As the executioners go to the dais to take Missy's body away, she wakes up and pushes them away. The Doctor reveals that he had sabotaged the execution machine into knocking Missy out instead of killing her. After scaring the executioners away, by tricking them into accessing his record of fatalities, The Doctor with Nardole's help, has her locked in a quantum chamber. This is the Vault under St Luke’s University in Bristol that they have been guarding.

Back in the real world, The Doctor finishes looking at the Extremis email and through the vault doors he asks Missy for her help to fight the forthcoming invasion. He asks her how he can save his friends when he is blind, saying ‘How can I save them when I'm lost to the dark?’.