The Doctor takes Clara to the command ship so that she can accompany him on the mission to discover why the Dalek, called Rusty by the Doctor, has become so damaged that it has, effectively, turned "good." How? Oh, only by shrinking down to almost microscopic size so that they can just walk right inside of the Dalek. Standard fare, no biggie. Accompanying the Doctor is Blue and two other soldiers to make certain that he is not a Dalek spy himself. The episode takes a unique change in direction as it portrays the entrance into the Dalek’s body as a 2001: A Space Odyssey method as it shows the Doctor and Clara floatingly enter through a blue wall into a black void. It is a shot straight out of the psychedelic and experimental, and easily one of the most memorable moments of an episode that seems to be making any excuse to show off the size of its budget. Inside Rusty, the series’ usual theme of idiot soldiers not listening to the Doctor and dying because of it continues as one of the soldiers behaves like an idiot and then dies for it when the Dalek’s antibodies take care of him. The rest flee into Rusty’s nutrient pool and work their way to its innards to discover the source of Rusty’s change of heart.
And then they make the mistake of fixing the damage that caused it. This turns Rusty back into its normal state—or, as the Doctor has been insisting all episode, its natural state. Rusty breaks free of its captivity and goes on a tear through the command ship, gunning down soldier after soldier in a series of shots that will further remind any longtime viewer of Nine’s "Dalek" episode, where the exact same thing happens. Rusty calls for reinforcements in the middle of its escape so that the human nuisance can be wiped out for good.
Back inside Rusty, the Doctor restates to Clara that this was inevitable. "There was never a good Dalek. There was a broken Dalek, and we repaired it." So Clara slaps him and angrily tells him that the notion of the Daleks being irredeemably evil all along is the exact opposite of what they really learned that day. The mirror between "Into the Dalek" and "Dalek" ends in this moment as the complete opposite consequences emerge from the otherwise similar events of both episodes. Whereas "Dalek" established that Daleks are irredeemably evil creatures with no recourse for vindication, "Into the Dalek" sees the Doctor try to find one way to make the Daleks into creatures that can have some small inkling of redemption.
The Doctor’s own little Away Team put their plan into action. Blue and Clara climb their way back to Rusty’s brain area after the other soldier, Gretchen Allison Carlisle, sacrifices herself to the antibodies so that they can make it there in time. In a very quick but no less important moment, Carlisle wakes up in heaven with Missy. The Doctor, meanwhile, makes his way to the actual Rusty organism’s chamber to confront it face-to-face. Outside the Dalek, the soldiers futilely fall back to organize their last stand as the Dalek army come bearing down on them.
NEXT: The Doctor clutches his totem