Two aliens, Andinio and her student Delph, arrive on a planet Andinio pronounces to be the end of their travels. Delph questions his ability to fulfill the task she has trained him for but she encourages him to believe in himself. He begins to telekinetically create something from the stones of the planet but is interrupted by a form taking shape behind them.

Jump forward 3,407 years and The Doctor and her Companions are receiving multiple distress signals from the planet of Ranskoor Av Kolos, which translates to "Disintegrator of the Soul."

The Doctor warns that the planet is putting out psychotropic waves and gives each Companion a neural balancer to prevent them from being affected by the waves.

The T.A.R.D.I.S. materializes in the holding bay of an abandoned craft. Paltraki emerges from the shadows with a weapon trained on the group. He has no memory of the rest of the crew or his own name. He discloses that there was a battle "outside" and that he could remember things before he went outside. Suddenly he acts as if he's seeing The Doctor for the first time again, having forgotten their conversation so far. The Doctor gives him a neural balancer. 

Yaz is able to activate the database and they discover Paltraki is the ship's commander and he had three crew members. The Doctor takes a look at the controls and discovers the ship is functioning perfectly. 

The neural balancer helps Paltraki remember his name. He joins at the controls as a call comes through. He moves everyone out of the viewing line and takes the call. He is commanded by a woman of the same alien background as Andinio and Delph to return because "The Creator" commands it. "The Creator" then commands his return and The Doctor recognizes the voice of Tim Shaw, the Stenza warrior encountered just after she regenerated.

Tim Shaw tells Paltraki to return what he took or his crew will suffer for it. He kills one of the crew when she advises Paltraki not to return. 

The Doctor asks what he has that Tim Shaw wants. Paltraki indicates a crystal with something inside it. The Doctor detects there's a bio-lock on it she doesn't understand and identifies it as Stenza technology.

Using Paltraki's mission briefing archives, they decide to retrace his steps. Outside the ship, Ryan starts to feel ill and Paltraki says the illness is how "it starts" while The Doctor deduces that the planet doesn't like intruders. Graham asks to speak to The Doctor alone. When the others move away, he tells The Doctor that if the Stenza holding the crew members hostage is Tim Shaw, he plans on killing him for him killing Grace. The Doctor tries to send Graham back to the T.A.R.D.I.S. but he refuses and states he understands that he won't be able to continue traveling with her if he kills Tim Shaw.

They come across the battlefield and Paltraki tells them they need to go to the giant floating stone structure beyond the battlefield. 

The Doctor sends Ryan and Graham to rescue the crew members and Paltraki and Yaz to fulfill the crew's original mission goal. She plans on finding Tim Shaw and finding out why he wants the crystal chamber. 

Standing below the stone structure, The Doctor manages to activate the entrance beam and the group is transported into the structure. The team splits up.

Ryan tries to convince Graham to give up his vendetta. While they're talking, a group of sniper bots approaches. They run but are blocked by another group. Trapped between the two squads, they duck and the two sets of bots take each other out. 

The Doctor is confronted by Andinio wielding a large gun. She points out that she'd attached grenades to the object so shooting her will only destroy the object. Although she won't say why the object is precious, she does introduce herself as Andinio of the Ux which is exciting news to The Doctor. When Andinio proceeds to demand the object, The Doctor tells her to show The Creator her face. When Tim Shaw sees her, he orders Andinio to brings The Doctor to him.

Paltraki's memories are coming back slowly as he and Yaz move through the ship. He remembers that his ship was part of the last fleet sent by the Congress of the Nine Planets in response to "the atrocities." Just then, sniper bots appear and he shoots two down. 

Yaz and Paltraki reach the crew's original mission goal, a chamber containing more objects like the one Tim Shaw wants back. 

Ryan and Graham reach the chamber their trackers show as holding the life signs. They find large crystal-shaped vessels holding Paltraki's crew members but there are others as well, over a dozen. 

Andinio escorts The Doctor to Tim Shaw who looks weakened and seems to be on a respirator. Tim Shaw orders Andinio to "ready him" which she verbally assents to but is unhappy about. Tim Shaw orders her out and she leaves The Doctor with him. He reveals that when she sent him back to where he came from, he landed on Ranskoor Av Kolos 3,407 years before they met and met Andinio and Delph who heralded him as The Creator and used their powers to create anything he wanted. And what he wanted was revenge.

While Ryan and Graham are trying to figure out how to free all the hostages in the stasis vessels, Ryan tries to convince Graham again that he shouldn't go after Tim Shaw, even admitting that he loves him like family now. 

Yaz contacts The Doctor about the other objects they've found but The Doctor puts her off. Paltraki notices movement and he and Yaz hide as Andinio comes in. She approaches a plinth where Delph is restrained to a device. He protests that he doesn't want to obey The Creator's orders but Andinio insists. 

The Doctor notices the ship shake when the Ux activate their power. Tim Shaw reveals that the shrine is actually the weapon and that he now takes whole planets as trophies. The object she's carrying contains a whole planet and so do the four in the Ux chamber. Tim Shaw intends on targetting Earth next. 

Ryan cracks the stasis vessel code and gets one of the crew members out. Tim Shaw is alerted to the release of his individual trophies and, in anger, disconnects his respirator tubes so he can go deal with them directly. 

Graham calls for help and Paltraki heads down. Ryan and Graham send all the captives with him to his ship. 

In order to disrupt the Ux capturing Earth, The Doctor and Yaz decide to transfer their neural balancers to Andinio and Delph. This will leave them vulnerable to the planets psychotropic waves. 

Graham insists that Ryan leave with the last of the freed captives. 

The Doctor adjusts the neural balancers into neural blockers and they work to stop the Ux from capturing Earth. The Doctor explains that Tim Shaw has taken advantage of the Ux's faith and turned Andinio and Delph into destroyers when they should be creators themselves. Yaz points out that the planets in the containers are starting to crack. 

By cobbling together the T.A.R.D.I.S.'s psychic circuits and the Stenza tech with the Ux powers, The Doctor attempts to send the five stolen planets back where they came from. It could kill the Ux but they're willing to try.

Meanwhile, Graham faces Tim Shaw and chooses not to fight him. Ryan comes in when Tim Shaw moves on Graham and Graham shoots the Stenza in the foot. They locked him into one of the stasis vessels and leave him there for a life sentence.

Paltraki intends to return all the freed captives to their homes, completing his mission. Delph convinces Andinio to leave Raskoor Av Kolos as well. They have sealed the ship so Tim Shaw will never be able to escape or be rescued. The Doctor and her Companions depart and The Doctor advises the Ux to keep their faith and to keep exploring.