Yasmin and Dan in the TARDIS

The Doctor and her travelling companion Yasmin Khan are in pursuit of Karvanista, a member of the dog-like Lupari species. They manage to escape from Karvanista’s capture and follow him to Earth in the TARDIS. En-route, The Doctor experiences a psychic vision of Swarm (a mysterious being who claims to share a history with The Doctor) escaping from its millennia-long imprisonment by the Time Lord Division. The TARDIS arrives in Liverpool just after Karvanista kidnaps the seemingly insignificant Dan Lewis for reasons that are at first unknown. Before leaving Liverpool, in pursuit of Karvanista, The Doctor and Yasmin meet Claire, a woman from their future and her past. Shortly afterwards Claire is touched by a Weeping Angel and is transported into the past.

On Karvanista’s spaceship, Yasmin rescues Dan while The Doctor confronts Karvanista over his connection to the Division and learns that the Lupari are in fact trying to save humanity due to Earth’s imminent destruction by the Flux, an unknown entity that defies all laws of space and time, as it consumes everything in its path. Meanwhile, the Flux causes Vinder, the sole crew member of a remote outpost in deep space, to evacuate and this event catches the attention of the Sontarans.

Following another psychic interaction between The Doctor and Swarm, the Flux accelerates its attack on Earth. The Doctor has Karvanista form a defensive shield with the other Lupari spaceships, protecting Earth from the Flux. Unable to transport behind the shield, the TARDIS is overtaken by the Flux. The Doctor releases some of the time vortex energy into the Flux, but this does not have any discernible effect. Then the TARDIS' doorways fly open as the Flux approaches.

Karvanista

The Doctor manages to land the malfunctioning TARDIS. On exiting The Doctor, Yasmin and Dan find themselves near Crimean War-era Sevastopol, where they are met by British General Logan and nurse Mary Seacole. The Flux's effects abruptly send Dan back to 2021 Liverpool, and Yasmin to a damaged temple full of dying priests. There she meets philanthropist Joseph Williamson and Vinder. Swarm arrives at the temple, reveals it to be on the planet Time, kills the priests and takes Yasmin and Vinder hostage.

Back on Earth, The Doctor discovers that instead of the British fighting the Russians they are fighting Sontarans who managed to slip past the Lupari's defences and overtake human history. The Doctor enlists Mary Seacole to gather intelligence on the Sontarans, while he summons the Sontarans to negotiate a retreat, only to be arrested by Logan's soldiers, who later fight a disastrous battle with the Sontarans. The Doctor regroups with Mary Seacole and the remainder of Logan's men, and they disrupt the Sontarans' supplies, but Logan reneges and bombs the Sontarans encampment so destroying their Spaceships.

Azure and Swarm

Meanwhile in Liverpool, in 2021, Dan discovers that the Sontarans have taken over his home city. He manages to infiltrate the Sontarans' shipyard but the Sontarans discover Dan's presence. Dan though is rescued by Karvanista who then destroys the shipyard, which resets the timeline. The Doctor manages to recover the TARDIS and collect Dan, but the TARDIS is hijacked and brought to the temple, where they are forced to watch as Swarm is about to kill Yasmin and Vinder.

The Doctor jumps into the temple's time storm and manages to stall Swarm by hiding Yasmin, Dan and Vinder in their pasts, albeit with many details changed. The Doctor jumps into her own timestream where she encounters memories of her past incarnation, the Fugitive Doctor, and Karvanista raiding the temple to defeat Swarm and rescue the priests. She finds the priests and encourages them to return to the temple, but the priests separate The Doctor from her past to protect her. The Doctor returns Yasmin, Dan and Vinder to the present and fixes the timestreams. She then returns Vinder to his Flux-ravaged home planet. But then a Weeping Angel intercepts the TARDIS.

The Doctor reboots the TARDIS, forcing the Weeping Angel out and stranding it in the village of Medderton in 1967. There Professor Jericho is conducting psychic experiments on Claire. While helping the villagers search for a missing girl called Peggy a Weeping Angel transports Yasmin and Dan back to 1901 Medderton where they find Peggy. They also discover a barrier to 1967 and Peggy's future self, who had to live out the rest of her life until then.

Sontaran

Still in 1967 Medderton, The Doctor, Claire, and Professor Jericho barricade themselves in the basement of Jericho’s house where Claire reveals she is becoming a Weeping Angel, having had a vision of a Weeping Angel that seizes her mind. The Doctor discovers the Weeping Angel is hiding from the other Weeping Angels, who are after it. The Doctor discovers that the rogue Weeping Angel has knowledge of the Division. When the Weeping Angels gain access to the house the group escape through a tunnel surrounded by more Weeping Angels, one of whom transports Professor Jericho back to 1901.

The Doctor learns the Weeping Angels have taken the village out of time to capture the rogue Weeping Angel. The rogue Weeping Angel reveals that it offered The Doctor to the Weeping Angels for its own safety. The Doctor is recalled to the Division as they turn her into a Weeping Angel, stranding the others in 1901.

The Weeping Angels transport The Doctor to the Division where she meets her adoptive mother, Tecteun, who reveals that the Division is their knowledge of the multiverse and that they orchestrated the Flux to kill The Doctor for interfering with the Division's plans. The Doctor also discovers that Tecteun has a fob watch containing her lost memories.

Vinder

Back on Earth in 1904, Yasmin, along with Dan and Professor Jericho, have been tasked by The Doctor, via a holographic message, to search for artifacts and psychics to discover when the world will end. They eventually arrive in Liverpool where they encounter Joseph Williamson who reveals to them, that while excavating tunnels under Liverpool, he has discovered several doorways that led to various other places and times.

Meanwhile over many decades, a snake-like entity, that calls itself the Grand Serpent, infiltrates UNIT as an officer, eliminating those who pose a threat to him. After being threatened by Kate Stewart, he deactivates all UNIT defences, allowing the Sontarans to invade Earth again.

Vinder discovers Swarm harvesting energy from Flux survivors, but is caught and trapped in a Passenger where he meets Dan's friend Diane who was kidnapped earlier by Swarm and Azure. The Doctor watches helplessly as Swarm arrives to disintegrate Tecteun and is about to do the same to her.

Time Priests

The Doctor splits herself into three copies. Azure attempts to return one of the copy's memories. Yasmin, Dan, Professor Jericho, and Joseph Williamson, use one of the doorways that Joseph Williamson discovered, to travel to 2021 where they meet Kate Stewart and the second copy of The Doctor, who tasks Professor Jericho and Claire to become captured by the Sontarans. The second copy of The Doctor then retrieves her TARDIS that Kate had kept safe. Meanwhile the third copy of The Doctor crashes Karvanista's spaceship into the Sontaran command. But it is caught in a shield protecting the Sontarans from such attack. The third copy of The Doctor and Karvanista are captured. The second copy of The Doctor manages to rescue the third copy but not before the Sontarans commit genocide against the Lupari.

The Doctor discovers that the Sontarans have offered an alliance with the Cybermen and Daleks - but this is a ruse to sacrifice them to the Flux while the Sontarans use the Lupari shield to protect them from the Flux, which destroys the Daleks and Cybermen. Claire manages to escape the Sontarans but Professor Jericho cannot. The two copies of The Doctor rescue Vinder and Diane, and reform the Lupari shield behind the Sontarans, leaving the Flux to consume them as well. The two copies of The Doctor then summon a Passenger which absorbs the Flux.

Azure and Swarm bring the first copy of The Doctor to Atropos to sacrifice her to Time, but Time destroys the duo and reunifies The Doctor. Using the tunnel doors, Kate and Vinder maroon the Grand Serpent on a small asteroid. Vinder and Bel (a survivor of the Flux who has been searching for Vinder as she is carrying his child) decide to travel with Karvanista. The Doctor invites Dan to join her and Yasmin in the TARDIS and while Yasmin shows Dan around the TARDIS, The Doctor deposits the fob watch containing her lost memories deep into the TARDIS interior.