- The Doctor's greatest enemy surrounds a rebel ship. To save everyone, he and Clara must choose to venture into the most dangerous place in the universe. The Doctor is forced to examine his conscience and ask if he is a good man.
- The Doctor saves Journey Blue, a rebel fighter, from her space shuttle, which is under attack by Daleks, but is unable to save her brother, who has already perished. He returns her to the rebel command ship Aristotle. He is greeted by Journey's uncle, Colonel Morgan Blue, who thanks the Doctor for saving his niece, but declares that he must be killed for fear he is a Dalek spy. However, Journey declares that, as he is a 'doctor', the Doctor can help their patient, which is revealed to be a war-torn Dalek they found floating through space who has appeared to have turned good.
Meanwhile, Danny Pink, a veteran of the war in Afghanistan with emotional scars from his past, 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. Feeling awkward due to an obvious connection between them, Danny declines, but when Clara finds him in his classroom despairing over his actions, she invites him out for a drink. He agrees, and she returns to her office, where she comes face to face with the Doctor, who she has not seen since he left her three weeks ago when he went for coffee in Glasgow (as seen in "Deep Breath"). He tells her that he needs her help, and asks whether he is a good man. Clara replies that she does not know.
They return to the Aristotle, where Colonel Blue details plans to miniaturize the Doctor, Clara, Journey and two rebel soldiers, Ross and Gretchen, so they can enter the broken Dalek, nicknamed Rusty, to see if they can determine what is making it good. Entering through the eyepiece, they begin exploring the upper part of the Dalek. Ross shoots a griphook onto the floor, and the Dalek releases antibodies, much like in the human body, which incinerate him. The Doctor, Clara, Journey and Gretchen flee to Rusty's waste centre, where the Doctor correctly guesses that nothing will be guarded. From there, they head to an area of high radiation, with Rusty speaking to the Doctor on the beauty it had witnessed in the galaxy, including the creation of a star, and that the Daleks must be destroyed for wanting to destroy that beauty. At the Dalek's power center, the Doctor discovers a large crack, which he deduces is causing the malfunction within the Dalek. He uses his sonic screwdriver to seal the crack, fixing Rusty in the process. However, this causes it to return to its normal thinking pattern, losing the good within it. Colonel Blue and his men are helpless as the Dalek breaks its chains and begins exterminating the rebels, determined to aid the Dalek cause. It contacts the Dalek main ship, which releases more Daleks with the aim of destroying the rebel command ship. Inside Rusty, Clara slaps the Doctor in the face and convinces the Doctor to try to reawaken the good side of the Dalek. They split up, with Clara and Journey heading to reawaken memories of the Dalek's past now being suppressed, and the Doctor heading to the Dalek's consciousness. Gretchen sacrifices herself to set up another griphook to get Clara and Journey to the mind of Rusty, but is destroyed by antibodies. She awakens after her death in "Heaven" and is greeted by a mysterious woman named Missy, the same woman who greeted the Half-Face Man ("Deep Breath").
Clara manages to awaken Rusty's memory of him seeing the creation of a star, while the Doctor manages to link his mind to Rusty's consciousness, reminding him of the destruction the Daleks caused. However, Rusty associates with the Doctor's own deeply-rooted hatred towards the Dalek race, and he exterminates his fellow Daleks as they attempt to destroy the rebel ship. On leaving the inside of the Dalek, the Doctor parts with Rusty, upset that the Dalek saw only darkness within him and wishing 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. Journey asks to come with them, but the Doctor declines, 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 the Doctor 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 says he is glad that his being an ex-soldier has not put her off. Remembering the Doctor's treatment of Journey, Clara tells Danny that she is not so judgemental.
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