The Doctor must confront the fact that Bill is now Cyber-converted and Missy is reunited with her less-than-sane past self, the Master, plus the threat of attack by the Cybermen.
Bill is hanging onto her humanity, but only barely. And Missy and the Master seem happy to all but flirt with each other over being evil.
The Doctor and Nardole decide to help a group of humans living in a simulated countryside while Missy and the Master take off to leave in the Master's TARDIS (despite an impassioned plea from the Doctor).
However, Missy, actually affected, fatally stabs the Master, forcing him to regenerate to survive. He returns the favor, but without the option of regeneration for Missy, because he would rather die than stand alongside the Doctor.
The Doctor sends Nardole with the villagers to another floor of the ship while he and Bill stay behind to handle the Cybermen. Eventually, the Doctor is overcome and fatally injured, so he destroys the entire floor.
Bill, overcome in the devestation and at the sight of the Doctor's body, is surprised when Heather, the pilot from the first episode of the season, appears and transforms Bill into a being like her.
They take the Doctor's body back to the TARDIS and go off together.
The Doctor revives in the TARDIS, but refuses to give in to regeneration. He stumbles out of the TARDIS, only to encounter his very first incarnation, who is also refusing to regenerate.