Missy, Nardole and Bill

The Doctor decides to test if Missy can turn good, despite Bill Potts' objections. Along with Bill and Nardole they answer a distress call and arrive in the TARDIS on a giant colony spaceship that is reversing away from a black hole. They are soon met by a blue skinned humanoid named Jorj who, fearing creatures that are arriving by the lift, holds them at gunpoint and demands to know which one of them is a human. Bill admits to being human. But, despite The Doctor's pleas, Jorj shoots Bill in the chest, mortally wounding her. The lift then arrives and humanoid figures, wearing masks and hospital gowns, exit and take Bill's body away claiming that they can restore her. As the lifts departs, to the lower levels of the spaceship, The Doctor telepathically tells Bill to wait for him.

The Doctor, Missy, and Nardole learn from Jorj that a few days ago, some of the human bridge crew had gone down to the lower level of the spaceship to start the engine reversal but they never returned. Jorj claims the spaceship was otherwise empty some days ago, but Nardole discovers there are actually thousands of life forms in the lower levels. They are the descendants of the first crew and, due to time dilation from the black hole, time moves faster at the spaceship's lower levels than the bridge. The Doctor incapacitates Jorj and, along with Missy and Nardole, departs below in a lift. As they leave the bridge Nardole, states that it has been ten minutes for them but he wonders how long Bill has been living below, to which The Doctor replies he hopes that they aren't too late.

Bill awakens in a hospital, where she finds that she has been fitted with a mechanical device that serves as her replacement heart. Razor, one of the hospital's employees, takes a liking to Bill and so shows her around. He explains that some of the patients are waiting to be ‘upgraded’ for Operation Exodus, to escape the polluted air of the spaceship's lower levels. He also explains to her how time passes really slow for them compared to the top. He shows her a live feed of the upstairs, which Bill then spends her time watching despite its extremely slow pace. Months go by with Bill eventually being put to work cleaning the hospital while plagued by The Doctor's message to wait for him.

Bill Is Shot

As more time passes Bill eventually convinces Razor to take her to the elevators so she can be transferred back upstairs. However, Razor tricks Bill into becoming the subject for the next ‘upgrade’. Unable to escape a surgeon remarks how the headpiece that he will fit on her head will inhibit emotion so she won't care for the pain of the process.

The Doctor, Nardole and Missy soon arrive, having come down the lift. While The Doctor and Nardole explore the hospital Missy tries to determine the origin of the colony ship. She finds that the spaceship is from the planet Mondas - the home world of the Cybermen.

The Patients

Razor approaches Missy and insists that she has been here before, and that The Doctor will never forgive her for what she did to Bill. When she denies it, Razor removes his disguise, revealing himself to be The Master, Missy's previous incarnation. Meanwhile The Doctor and Nardole find an operating theatre where a Mondasian Cyberman, from when The Doctor first encountered them, emerges from a closet. Backing away, The Doctor confirms he means no harm and asks for Bill's location. To his horror, the Cyberman asserts that it is Bill. Missy, accompanied by The Master, then arrive - the latter surprising The Doctor. The Master explains they are all witnessing the genesis of the Cybermen. Bill, as a Mondasian Cyberman, tells The Doctor that she waited for him. While underneath the Cyberman’s face cover, Bill sheds a tear.

The Master and Missy restrain The Doctor, However, unknown to them he had earlier managed to change the Cybernet to perceive Time Lords as convertible humans. On the roof of the hospital they soon find themselves besieged by Cybermen. Missy knocks out The Master and frees The Doctor, who wonders whose side she is actually on. Nardole then arrives in a commandeered shuttlecraft, but The Doctor is electrified by a Cyberman before he can escape. Missy and The Master try to trick Nardole into abandoning The Doctor, but the Cyberman, that was Bill, prevents the shuttle from leaving by grabbing onto the ladder until she and The Doctor are aboard.

The shuttlecraft takes them to a higher floor on the colony ship, where time moves slower. They find themselves on a solar farm where a human community, with a large number of children, protect themselves from early Cybermen prototypes from Operation Exodus. The time on the new level allows The Doctor to recover but he starts to show early signs of regeneration which he manages to suppress. Bill regains her human consciousness through her strength of will, despite still being a Cyberman. She perceives herself as being fully human until Alit, one of the children, gives her a mirror, so revealing the truth that Bill is a Cyberman. Bill sheds a tear when she realises the humans are frightened of her. The Doctor wipes it away, noting it is very unusual for a Cyberman to show such emotion.

Missy, Cyber Bill and The Master

Missy discovers a camouflaged lift in the nearby forest but, when she summons it, it brings up an advanced Cyberman from the lower floor, which they quickly destroy. Missy suggests they can all use the lift to escape to the bridge and The Doctor's TARDIS. The Doctor warns them that the time dilation below affords the Cybermen more time to develop and strategise and so they must prepare for a battle.

Nardole discovers that the floor below the one they are on has many fuel pipes that could be detonated remotely and so could be used as a weapon against the Cybermen. The Doctor also finds a conduit to another solar farm on a higher floor that can be used to evacuate the children. The Master and Missy meanwhile, decide to leave and plan to find The Master's TARDIS at the lowest floor, despite The Doctor's impassioned plea for them to stay and help.

An initial wave of Cybermen then arrive, and using Nardole's tricks with the explosives, they are able to make it seem that the humans appear more powerful. This forces the Cybermen to retreat and develop a new plan, giving the humans more time. Knowing this ploy has only served to delay their inevitable defeat, The Doctor instructs Nardole to lead the children to a solar farm on another floor and to then look after them. Against Nardole's protests The Doctor intends to stay alone to fight the Cybermen but Bill insists on staying with The Doctor to fight the Cybermen.

Cyber Bill

At the lift, Missy betrays The Master and fatally stabs him, forcing his next regeneration to begin, where he will regenerate into her. Leaving The Master inside the lift Missy says she will return to stand with The Doctor. An appalled Master, however, fires his laser screwdriver at her once her back is turned. The intense full blast fatally injures Missy and disables her regeneration. Each of them laugh as she starts to die and the lift doors close with The Master inside.

With all the humans evacuated, The Doctor engages the final wave of Cybermen by igniting all the pipes below the floor, engulfing everything in a wave of destruction. All the Cybermen are killed, but The Doctor is severally wounded. Bill, still as a Cyberman and the sole survivor, comes to mourn over The Doctor's body, but suddenly she finds herself out of the Cyberman suit, seemingly human. Heather (who she met in "The Pilot") appears from a nearby puddle. Heather explains that she located Bill through the tears that she had placed on her and has transformed Bill into an entity like herself. They take The Doctor's body into the TARDIS, and Heather pilots the TARDIS to a new location. Heather then offers Bill to live out a different life and to explore the universe, which Bill accepts.

Unaware of what has happened to Bill, The Doctor regains consciousness and starts regenerating. He tries fighting it off, recalling the last words of some of his previous incarnations in his confusion. He manages to control the regeneration, angrily stating that he does not want to change again, hating the fact that he must become someone else. He steps outside the TARDIS, into a snowy landscape, and fully halts the regenerative process by shoving his fists into the snow. He then hears a voice in the distance stating the same words of not changing. The Doctor calls out to the person and from out of the snow the stranger appears and asks for The Doctor's identity, which he confirms. The stranger replies that while The Doctor may be a Doctor, he 'is The Doctor, the original you might say'. Much to The Doctor's shock and surprise the stranger is revealed to be his first incarnation - the First Doctor.