This is a continuation from the previous episode, Extremis. It begins with Bill Potts with her girlfriend Penny strolling along and talking about what has happened. When they get back to the house, the house is invaded by soldiers from the United Nations and the U.N. Secretary General walks in and tells Bill that The Doctor is needed.
The Doctor finds that the Tardis is now onboard a plane with Bill Potts on its way to Turmezistan where a Pyramid has appeared out of the blue. The zone is a war zone between the three most powerful armies of the world, the Americans, the Chinese and the Russians.
The Occupants of the Pyramid, the Monks want to take over the planet but only if the people of the planet consent to being taken over and live by the Monks rules. Representatives of the three armies along with The Doctor visit the Pyramid after the Doctor went on his own and failed. The Monks show the representatives what will happen if the planet doesn't consent, the planet has become a wasteland.
The time on peoples watches keep changing and moves to three minutes to midnight, the time that is supposed to represent the end of life on earth due to war or other man made incident. The Americans plan to bomb the pyramid doesn't go to plan as the planet is landed forcibly and the submarine that the Russians had planned to fire a missile from is "landed" next to the pyramid. All the people in the planes and submarines are released by the Monks unharmed.
The Doctor works out that the end of the world event isn't the war between the armies but a virus that has been accidentally created. The Doctor sets about to work out where the virus will be created with Nardole's help. The Doctor disables the video feeds of all the laboratories that could possibly be the cause of the virus. The Monks trn back on one of the feeds which leads the Doctor to visit.
In addition to the Doctor we followed a female scientist whose glasses got smashed as she left for work. It is implied that because she didn't have good vision, she inadvertently created the virus that would destroy life on Earth by getting her numbers wrong. A colleague of the scientist dies and is the first death.
When the Doctor arrives, he set about destroying the virus but he accidentally gets on the wrong side of a fire door and because he's blind, he can't see the digits of the lock to escape. When Bill hears that the Doctor is blind and can't escape, she goes to the Monks and surrenders for the planet. Unlike the other people who had surrendered to the Monks, Bill's surrender was real and was accepted by the Monks.
As part of the surrender, the Doctor gets his sight back as Bill asked for.