The Doctor and Clara are on the most beautiful train in history, speeding among the stars of the future. But a deadly creature is stalking the passengers. Once you see the horrifying mummy, you only have 66 seconds to live. No exceptions, no reprieve. As the Doctor races against the clock, Clara sees him at his deadliest and most ruthless.
In the weeks following the events of “Kill the Moon”, Clara has come to realise she does not hate the Doctor for taking her into dangerous situations, though her boyfriend Danny Pink urges her to stop traveling with him. Clara allows the Doctor to take her on one “last hurrah”. They arrive via TARDIS in the future aboard a space-bound train that has been modeled after the Orient Express, with many of its passengers in period outfits.
They learn of the death of the elderly Mrs. Pitt, who died after claiming to have witnessed a mummy attack her. The Doctor, posing as a mystery shopper, talks to Perkins, the train’s engineer, who is also curious to her death and is suspicious of the train and its automated computer system, Gus, and provides the Doctor with various manifests to study. Meanwhile, Clara speaks to Maisie, Mrs. Pitt’s granddaughter who is traumatized by her death, and has been trying to see her body. In their search, they become trapped in the storage car, where a sarcophagus sits, and the two bond as they wait for rescue. A chef on the train dies from a heart attack after claiming to have seen a mummy. The Doctor reviews video footage and finds that both deaths occurred exactly 66 seconds after lights flickered nearby; this follows from a myth that Prof. Moorhouse reiterates about the legend of a supernatural being called the Foretold. Clara is able to make contact with the Doctor, but when he goes to rescue her, the lights nearby flicker, and the sarcophagus begins to open. Fearing that Clara is the next victim, he tries to unseal the storage door but is stopped by Captain Quell, who has determined his credentials are fake and charges him with the murders. However, when one of Quell’s men dies after 66 seconds, Quell realises the Doctor is innocent and lets him go.
The Doctor addresses the assembled staff and passengers, stating his belief that there is something odd about this train including the large number of scientists aboard the train. The illusion of the Orient Express disappears, as well as several holographic passengers, revealing them to be in a laboratory; Gus informs the passengers they are now to study the Foretold as to reverse engineer whatever technology it uses. The Doctor calls down to Clara, finding that she and Maisie have found documentation that the sarcophagus is for capturing the Foretold, and this is not the only attempt to do so by whatever agency that controls Gus. When the Doctor spends too long talking to Clara, Gus demonstrates its ruthlessness by opening the kitchen car to the vacuum of space, killing the staff, and threatening to kill more.
Prof. Moorhouse is the next target of the Foretold, and the Doctor and Perkins use his death to identify that the Foretold is draining energy from its victims using phase-shifting technology that takes about a minute to complete. Perkins also identifies that the victims have been the medically weakest on the train. Captain Quell realises he is next due to his post-traumatic stress disorder from a war, and when the Foretold comes for him, he is able to retain his senses long enough to provide the Doctor confirmation of his theory. When Perkins identifies that Maisie is likely next due to her trauma, the Doctor convinces Gus to allow Clara to bring her to the laboratory. En route, Clara sees the TARDIS blocked by a force field. By the time they get to the Doctor, Clara has realised that Gus is aware of who the Doctor is, and that the Doctor had purposely brought her here into another dangerous situation. As the two argue, Maisie reports seeing the Foretold; the Doctor quickly draws on her memories to trick the Foretold into targeting him instead. In the 66 seconds the Doctor successfully identifies the Foretold as a modified stealth soldier of a long-ago war, and offers their surrender as to make the Foretold believe the war is over. The Foretold becomes visible to all, salutes the Doctor, and then disappears into a pile of dust, leaving behind its phase-shifting device.
Gus congratulates the passengers on their success and then evacuates the air on the train as their services are no longer needed. While Clara and the others pass out, the Doctor rigs the phase-shifting device into a short-range teleporter and evacuates the surviving passengers to the TARDIS before the train explodes. On a nearby planet, Clara regains consciousness while the Doctor explains he has returned the passengers to a nearby city, and regrets that he could not hack into Gus in time to find who was responsible for the train before the attempt triggered the train’s destruction. Clara and the Doctor talk about his actions and his apparent heartlessness towards the passengers he could not save, but the Doctor explains that doing the right thing sometimes means making hard choices. As they prepare to leave, the Doctor offers Perkins, who he has come to respect, a job to maintain the TARDIS but Perkins politely declines. Danny calls Clara to ask if she has said her final goodbyes to the Doctor. As she hangs up, she lies and admits to the Doctor that Danny accepts her continuing to travel with the Doctor, and tells the Doctor to “shut up and gimme some planets”.