Sometimes when you think the plot of a story goes one way, it goes in a completely different place. This is certainly true this week on Doctor Who, where he’s trying to translate an ancient book that causes those who read it to kill themselves.

Or is it?

At least we do know for sure who’s in the vault.

SPOILERS BELOW

The Doctor still hasn’t told Bill he’s blind, and won’t because he doesn’t want her to worry. He gets a visit from the Pope (honest!), who asks him to translate a book called “Veritas”. His assistants tell him those who have tried to translate it have wound up killing themselves. Another group apparently did the same thing a few months before, but one of them is missing. The Pope sought the Doctor thanks to a recommendation from Pope Benedict IX in 1045. It’s implied that Pope was a woman, but that isn’t true (although there are rumors there was one).

Soon the Doctor and Nardole (Matt Lucas) zip to Bill’s (Pearl Mackie) flat, where she’s having tea with a new friend named Penny. That stops fast when the Pope (Joseph Long) suddenly shows up. It’s a classic scene.

The group heads to a special library of the “heretical books” of the Vatican. They find the missing priest, who confesses he downloaded his translation to the internet. He later kills himself as Nardole and Bill discover. It’s been read by a group of physicists called CERN, and their response is strange. Meanwhile, it looks like some portals are opening, and someone grabbed Cardinal Angelo (Corrado Invernizzi) through a wall.

While this is going on, there are flashbacks to what looks like the execution of a Time Lord. It seems to be the Doctor, as an executioner named Rafando (Ivanno Jeremiah) tells him how a Time Lord is killed, and that another Time Lord must be present.

That’s when Missy (Michelle Gomez) shows up…and it’s actually her execution. She’s surprised to see him, thinking he’d retire to Darillium with his wife. Then she figures out River is dead.

Strangely enough, she actually begs for his help. She promises she’ll be good, or at least take lessons. She even insists that she is his friend. As she puts it, ” without hope, without witness, without reward, I am your friend.” That will be important, but more on that later.

Meanwhile, Nardole and Bill go through a portal, and find themselves in the Pentagon. Apparently there’s a room where there are lots of portals to different places. They track down the physicists at CERN, who apparently plan to blow themselves up. They don’t seem to be worried, when Nicolas (Laurent Maurel), one of the physicists, challenges Narolde and Bill to think of any number, and they come up with the same number, over and over. They think they’re in a fake world, and that’s why they blew themselves up.

It gets worse. Nardole wonders if they are real. Standing next to a projector, he finds out he isn’t. This shocks Bill, but she follows a trail of blood to a portal. She finds the Doctor at the Oval Office, next to the body of the President.

All this time, he’s been trying to restore his eyesight, at the cost of his future selves. He doesn’t succeed, but seems to see blurry forms…of someone. It’s actually zombie monks, who get their hands on the Veritas. The Doctor has the computer version, but can’t see. He does get help from another computer program that reads the text to him.

He learns the story is about a demon, or rather an alien, who wanted to take over the world. So, he had a “shadow world” to perfect its plan. Thus, those who read the text and killed themselves think they were fake people trying to escape a fake world. Come to think of it, are the Doctor and Bill real or not? Bill suddenly learns she is fake.

All that’s left is the alien and the “Doctor”. It vows to use its “fake Earth” to conquer the real thing, and the “Doctor” wishes he could be turned off since he has no hope.

Amazing, isn’t it? The story starts with a deadly book that kills whoever reads it, and ends with the shocking revelation that the world may be a computer program used by an alien to wants to take over the real thing.

That’s quite a twist, and writer Steven Moffat should be commended for it.

So how does the “Doctor” do?  He goes back to what Missy said (“without hope, without witness, without reward”), and he decides it doesn’t matter if he’s real or not, he’s still the “Doctor”.  He literally sends an e-mail to his real self, and tells him what the alien Monk plans to do. It’s like sending a distress signal to real SHIELD agents from the Framework. Not bad.

So, what happened to Missy? Well, the execution is interrupted by a priest, who tells the Doctor “virtue is only virtue in extremis.” That came from River Song’s diary, and it turns out the priest is Nardole. He says River sent him, and gave him permission to clobber the Doctor. This apparently took place after last Christmas’ episode.

Finally, Missy is executed, and the Doctor promises to guard her body for a thousand years. Then it turns out she isn’t dead. He decided to let her live, but she’ll have to be in a vault.

Yes, THAT vault. For the record, we called it two weeks ago, especially when she apparently played “Pop Goes The Weasel” in there at the end of “Knock Knock”.  The only question is, will that decision backfire? Maybe. Then again, he’s always had a bit of respect for his best enemy, the Master/Missy.

As for the executioners who want Missy to die, the Doctor asks them to look up how many people/aliens he’s killed. It’s enough for them to back off. More than enough.

Aside from this wild twist, viewers should also praise Pearl and Matt for their scenes together as they try to process what’s happening, and especially Matt for revealing he has the right to clobber the Doctor if necessary and might do the same to Bill if she doesn’t listen to him.

Somehow, the Doctor must stop the alien Monk from taking over the world for real by having humanity die by its own hand…as if it just read the Veritas. However, he admits to Missy through the vault that he feels lost about what to do because he’s blind.

He has to think of something, especially when a pyramid appears from nowhere. Maybe he’ll also tell Bill the truth.