In World War II London, soldiers are working in a bunker during a bombardment when Prime Minister Winston Churchill arrives. They inform him of the situation and he tells them that it's time to roll out the secret weapons. They smile and position a model of a Dalek on the tactical map.
The TARDIS materializes inside of the bunker and the Doctor emerges to find soldiers waiting for him. Churchill is with them and the Doctor introduces him to Amy. Churchill jokingly asks for the TARDIS key and the Doctor refuses. As they go to Churchill's office, the Prime Minister explains that he called the Doctor a month ago. They meet Lillian, one of the staff officers, who appears depressed but cheers up with some encouragement by Churchill. The Prime Minister then tells the Doctor that with the imminent thread of invasion, he'll embrace any possibility.
They go to the roof and Churchill introduces the Doctor and Amy to Professor Edwin Bracewell, head of the Ironside Project. He's watching as German Stutkas advance and begin bombing. Bracewell gives the order to his new weapon to fire, and an energy beam destroys the Stutkas. The Doctor realizes that there's advanced technology involves and Bracewell orders the new secret weapon to advance: a Dalek. The Dalek apparently does not recognize the Doctor, who confronts it. Bracewell explains that it's his Ironside, and tells it that it will help the Allied cause. The Dalek agrees and insists it will win the war.
Below, Churchill shows the Doctor Bracewell's blueprints and explains that the professor invented them. The Doctor explains that they're alien. A Dalek passes behind them as the Doctor warns that they are entirely hostile, but Churchill insists they will help win the war. When the Doctor wonders why Churchill called him, the Prime Minister admits that he initially had doubts but now believes an army of a hundred or a thousand could win the war. The Doctor turns to Amy to have her describe the invasion in her time period, but she has no idea what he's talking about. He realizes that it isn't possible.
In the war room, the Doctor watches and wonders what the Daleks are up to. Amy asks one of the Daleks if it is an alien. It merely insists that it is a soldier for the United Kingdom. The Doctor tries to convince Churchill he's making a mistake, but the Prime Minister insists that he can save millions of lives and he would deal with the Devil himself if necessary. The all-clear alarms sound and the Doctor tells Amy that he's going to prove the Daleks are dangerous. He goes to Bracewell's laboratory and asks how the professor came up with his ideas. Bracewell says that ideas just come to his head, and displays a variety of futuristic blueprints. The Doctor warns him that the Daleks can't be trusted. Churchill arrives and the Doctor snaps at the Daleks, demanding answers. It claims ignorance and the Doctor attacks it with a spanner. He tries to provoke it into killing him, stating that he is the Doctor and has defeated the Daleks repeatedly. It finally says that it has recorded his testimony and transmits it to a Dalek saucer hiding behind the Moon.
Aboard the saucer, another Dalek broadcasts the Doctor's testimony to the "Progenitor."
Churchill calls in the marines, which the Daleks quickly kill them. Bracewell insists that he is their creator, but they blast off his arm, revealing circuitry. They explain that they created him, declare victory, and teleport away. The Doctor realizes that he was their plan. He run out.
Aboard the saucer, the Daleks arrive and watch as the Progenitor activates.
The Doctor goes to the TARDIS and Amy insists on going, but he tells her to stay behind and departs. He follows the signal to the Dalek saucer.
Lillian reports to Churchill that there is an unidentified object hanging in the sky. They realize the Doctor is aboard the Dalek saucer.
Atop the bunker, an air warden watches the sky.
Aboard the saucer, the final phase commences and the Daleks channel all reserve power to the Progenitor. The TARDIS arrives and the Doctor steps out. He threatens them with the TARDIS self-destruct device and they back away. The Doctor examines the ship and realizes that it's on its last legs and they were dying. They explain that they detected a Progenitor device and follow it into the past. It contains pure Dalek DNA and all were lost except one. The Doctor wonders why they created Bracewell, but they refuse to explain, and he realizes that the Progenitor considered them impure. They needed to lure the Doctor to London to testify so the Progenitor would accept them as real Daleks. One of the Daleks then activates a console and informs the Doctor that since they don't have the power, they will trick the humans into destroying themselves.
All of the lights in London turn on and Churchill realizes that the Germans will quickly move in and attack. They spot German bombers, 10 minutes away. Amy says they need to take the fight to the Daleks, and she remembers the plans that Bracewell showed them earlier.
The Doctor tells the Daleks to turn off the lights or he'll destroy them, but they tell him to leave. Once he does, they will return to their own time and begin the recreation. The chamber opens as the Daleks announce that DNA reconstruction is complete. A new Dalek paradigm emerges: a white Dalek in a new casing. Four others emerge behind it: blue, yellow, orange, and red.
Churchill and Amy go to the lab, where Bracewell is contemplating suicide. He insists that he can remember his "life," and wonders what he is. Churchill asks what side he's on, and Amy takes the gun away. She explains what is happening and that he is the only one who can help them. Amy reminds him that he had developed missiles, and Churchill and Bracewell seize on her plan and propose they launch the missile at the Dalek saucer.
The new Daleks declare their predecessors as inferior and destroy them. They advance on the Doctor, who threatens them with the self-destruct.
The German bombers close in as Bracewell creates a device to pick up the Daleks' transmissions, and watch as the Doctor confronts the newest incarnations of his enemy. They realize the "self-destruct device" he's holding is a Jammie Dodger, but detect approaching objects. They receive a transmission and the Doctor confirms that they're British pilots, flying three fighters designed to navigate in space. He tells them to destroy the saucer and runs off, avoiding Dalek fire.
The British fighters open fire and try to take out the Dalek energy pulse. Two of them are destroyed and the final one is unable to penetrate the shields. The pilot contacts the Doctor, who has made it to the TARDIS. He informs him that he can disrupt the shields momentarily, and the pilot makes his attack run. He destroys the energy pulse device and the lights go out in London. The Doctor tells him to destroy the ship, assuring him he'll be fine. The Daleks contact the Doctor within the TARDIS and tell him to call off the attack or they'll destroy Earth. The Doctor doesn't believe them, but the Dalek explains that Bracewell is a bomb. He doesn't want to let them go, realizing they will begin again, more powerful than ever. The Daleks begin the countdown and tell the Doctor to choose. He finally tells the pilot to withdraw and then takes the TARDIS back to London.
Upon arrival, the Doctor finds Bracewell and knocks him down, and explains that he's a bomb. He opens Bracewell's chest, realizing the Daleks have activated the bomb anyway. He works to deactivate the bomb while explaining that stolen memories were planted in the Bracewell robot's positronic brain. The Doctor tells Bracewell to relate his memories and prove he is human. Despite the emotional pain, the Doctor insists he believe he is human, and use his human will to stop the bomb from detonating. Amy lends her efforts and talks to Bracewell of the pain of losing someone. When Bracewell remembers Dora Bella, the woman he lost, the countdown slows and then finally stops.
The Daleks realize that the bomb has deactivated and escape via a time corridor. Bracewell senses their departure and tells the Doctor. The Time Lord is furious, and despairs that he has unleashed a new threat upon the universe. Amy and the others finally manage to comfort him, assuring him that he managed to save the Earth once more.
The next day, the Londoners recover and Amy notices that Lillian is crying because her boyfriend was shot down over the Channel. The Doctor informs them that he's removed the advanced technology, but assures Churchill that he will eventually triumph without it. Amy and the Doctor make their farewells, and Amy catches Churchill as he tries to steal the TARDIS key. They go to the laboratory where Bracewell is waiting for them. He expects the Doctor to deactivate him, and the Doctor assures him that he'll be back eventually to deactivate him. First he and Amy have to see to a few things in the TARDIS, but they tell him not to go off in the meantime. Bracewell finally realizes what they mean and thanks them.
As the Doctor and Amy enter the TARDIS, Amy notes that he has arch enemies and it's not all fun and travel. She insists on staying and wonders if he's worried about the Daleks. She notes that it will take time for them to build forces. However, the Doctor is more concerned that Amy doesn't remember the Daleks from her time. As they leave, they are unaware that there is a time crack in the wall behind them.