The Doctor and Clara find themselves inside of a supposedly good Dalek.
The Doctor saves rebel fighter Journey Blue from her space shuttle, which is under attack by Daleks. He returns her to the rebel command ship Aristotle, a former hospital ship converted for military use. To prevent his being executed as a potential Dalek spy, Journey offers the Doctor’s services to assist with their “patient”: a damaged Dalek the rebels found floating through space. This Dalek, surprisingly, declares that the Dalek race is evil and must be destroyed. Somehow, the damage inflicted upon it has given it a sense of morality — a “good” Dalek.
Meanwhile, Danny Pink, an Afghanistan war veteran emotionally scarred from his experiences, begins teaching Maths at Coal Hill School. In the staff room, Danny is introduced to Clara Oswald, who invites him to a leaving do for one of their colleagues. Danny declines, feeling awkward due to an obvious connection between them. However, when Clara finds him in his classroom despairing over his actions, she invites him out for a drink instead. He agrees. Back at her office, Clara comes face to face with the Doctor, whom she hasn’t seen in three weeks since he left her to get coffee in Glasgow (as seen in “Deep Breath”). He tells her that he needs her help. He begins by asking her for her honest opinion: is he is a good man? Clara hesitantly replies that she doesn’t know. The Doctor then briefs her on what happened aboard the Aristotle. Clara agrees to assist his efforts to help the “good” Dalek, despite the Doctor’s contention that Daleks cannot be turned good.
Back at the Aristotle, the Doctor, Clara, Journey and two rebel soldiers, Ross and Gretchen, are miniaturised so they can enter the broken Dalek — nicknamed “Rusty” by the Doctor — to determine what is making it good. Entering through the eyepiece, they begin exploring the upper part of the Dalek. They come upon its “cortex vault”, which the Doctor describes as Dalek technology designed to suppress any developing compassion within the living mutant inside the shell, as well as store all of its memories. Ross shoots a griphook onto the floor, and he is incinerated by autonomic antibodies, much like in the human body. The Doctor coldly uses Ross’s death to lead the others to Rusty’s waste centre, which he correctly concludes is unguarded. From there, they enter an area of high radiation. Rusty, speaking to the Doctor, relates the beauty it had witnessed in the galaxy, including the creation of a star. Rusty drew from this that Daleks must be destroyed for wanting to destroy that beauty. At Rusty’s power center, the Doctor discovers a large crack leaking radiation, causing the malfunction within the Dalek. He uses his sonic screwdriver to seal the crack and repair the damage. However, this unintentionally causes the Dalek to revert to its normal thinking pattern, losing the good within it.
The rebels are helpless as the Dalek breaks its chains and begins exterminating them. Determined to aid the Dalek cause, it contacts the main Dalek ship, which sends other Daleks to destroy the rebel command ship. Inside Rusty, Journey and Gretchen plan to destroy the creature from the inside. Clara, appalled by the Doctor’s callousness during the entire mission, slaps him in the face and convinces him to reconsider his conviction that Daleks are “irreversibly evil”. He persuades the soldiers to try and reawaken the Dalek’s morality. They split up, Clara and Journey heading for the cortex vault to revive Rusty’s past memories now being suppressed, and the Doctor preparing to link with the Dalek’s consciousness. Gretchen sacrifices herself to set up another griphook to get Clara and Journey back to the upper level, and she is destroyed by antibodies. She awakens after her death being greeted by mystery woman Missy at a breakfast table in “Heaven” (“Deep Breath”).
Inside the cortex vault, Clara manages to awaken Rusty’s memory of seeing a star’s creation. The Doctor then links his mind to Rusty’s consciousness, showing him the beauty of creation and life, along with the destruction the Daleks caused. However, Rusty not only regains his morality, he also assimilates the Doctor’s own deep-rooted hatred towards the Dalek race. He exterminates his fellow Daleks as they attempt to destroy the rebel ship. After leaving the inside of the Dalek, the Doctor parts with Rusty, disturbed that the Dalek saw only darkness within him; he’d hoped for a ‘victory’ in creating a ‘good’ Dalek. Rusty’s response is that the Doctor himself is a good Dalek, while Rusty is not. Rusty sends a signal to the Dalek mothership, causing it to believe the Aristotle has self-destructed, and vows to continue with his mission to destroy the Daleks.
The Doctor and Clara depart. Realising she is not a soldier at heart, Journey asks to come with them. The Doctor turns her down, telling her that though she has a kind heart, he wishes that she hadn’t been a soldier. The Doctor returns Clara to her office, moments after she left. Clara tells him that, although she is still unsure of whether he is a good man, she knows his intentions are well-meant. On leaving, she bumps into Danny, who is glad that his being an ex-soldier hasn’t put her off dating him. Remembering the Doctor’s treatment of Journey, Clara tells Danny that she is not so judgemental.