Aboard the Dalek command saucer, the Daleks detect the TARDIS in flight and prepare to open fire. The missiles impact the TARDIS and explode, but Jack and the Doctor dematerialize before impact and rematerialize on the saucer... around Rose and a Dalek. Jack shoots and destroys the Dalek, and the Doctor embraces Rose.
The Daleks observe the TARDIS and wait patiently.
The Doctor explains that the Daleks left to fight the Time War, and he was there when his people were destroyed and took the Daleks with them. Rose warns that there are thousands of Daleks, and the Doctor decides to go out and confront them. They open fire only to discover that he's protected by a forcefield. The Doctor asks how they survived, and the Emperor Dalek reveals itself to inform him that they survived through him. It says that its ship survived when it fell through time, and it cultivated and dissected humans to create a new human race. Now the Emperor Dalek considers itself a god, and the Doctor realizes that it has gone insane. The Doctor, Jack, and Rose leave despite the Daleks' protestations.
The Doctor returns to the Game Station and tells them to turn off all broadcasts and transmitters. He realizes that the planet is defenseless, and wonders why Lynda is still on board. They explain that a hundred people are still stranded on Floor Zero.
The Emperor Dalek orders the Daleks to attack, saying that Earth will become their paradise once it is sterilized.
The Doctor goes to work trying to rewire the station, and explains that he plans to generate a delta wave, which will fry any brain in its path. However, it would normally take three days to rewire, and they only have 32 minutes until the fleet arrives.
Jack rewires the station forcefield to prevent the Daleks from blasting it to pieces, but warns that they can still board. They have to get to Level 500, and Jack concentrates the extrapolator at 494, forcing them to fight their way up to 500. While Rose helps the Doctor, Jack arms the others with the guards' guns, which are sufficient to destroy the Daleks. Lynda promises the Doctor that she will do her best and goes with the others. Jack kisses them both and admits he was better off as a coward, then goes to fight with the others. Rose wonders if he'll be all right, but the Doctor doesn't respond.
Jack talks to the humans on Floor Zero and gets their attention by opening fire. He then asks for volunteers and warns that an army is going to invade the station. Rodrick insists that the Daleks disappeared years ago and most of the humans agree with human. Jack tells them to stay quiet and listen as they die, and wonder then if the Daleks are real.
As the Doctor works, Rose wonders why the Doctor doesn't go back in the TARDIS and give a warning. He notes that they can't without altering the timeline, and suggests they leave. Rose says they can't, and the Doctor agrees, pointing out she never asked. The delta wave starts to build and the Doctor gets an idea. He says he can use the TARDIS to cross his own timeline and use the delta wave. He gets her into the TARDIS and then tells her to wait, goes outside, and activates the TARDIS by remote. By the time she realizes what he's doing, she's unable to get out as the TARDIS dematerializes.
An emergency hologram of the Doctor comes on and informs her that he has engaged Emergency Program 1, designed to keep the TARDIS from falling into enemy hands. It will take her home, and the message tells her to let it be forgotten and gather dust until it's buried and gone. Finally he ends by telling her to remember him by having a good life. Rose insists he can't do that to her and tries to operate the TARDIS controls to take her back.
The TARDIS lands and she finds herself back in her own time and place. Mickey hears the engines and arrives as she steps outside, crying.
Jack calls Rose and the Doctor informs him that she's gone and won't be coming back. He realizes that the Doctor took her home, and asks if the delta wave will be ready. The Emperor Dalek sends a broadcast telling the Doctor to explain that the delta wave must kill everything in its path, human and Dalek alike. Jack realizes the transmitter will blanket Earth, and the Doctor insists that humanity can survive on its colony, but the Daleks are gathered here and now and this is his one chance to wipe them out. Once Jack is sure that Rose is safe, he tells the Doctor to go ahead, much to the Emperor Dalek's surprise. The Doctor then asks what "Bad Wolf" means, and the Emperor Dalek says it had nothing to do with it.
Jackie and Mickey take Rose out for a meal and talk of everyday things. She can't forget that the Doctor is dying 200,000 years in the future, and she's just sitting there. Jackie insists the Doctor did the right thing by sending Rose back to her, but Rose can't accept returning to an ordinary life. Mickey wonders if she thinks she's better than the rest of them, and Rose tries to explain that the Doctor showed her a better way of living her life without giving up. She angrily gets up and runs out.
Jack stations Lynda on the top floor with orders to watch out for the Daleks and keep him advise. The Dalek fleet arrives and the Daleks descend on Earth in the thousands.
Mickey goes to find Rose and tells her she has to forget and find a normal life. Rose notes "Bad Wolf" written on the concrete in huge letters and similar graffiti written all around. She realizes that it's a message, a link between her and the Doctor 200,000 years in the future. Rose realizes that it means there's a way for her to get back.
The Daleks begin invading the station.
Inside the TARDIS, Rose explains to Mickey that the vessel is alive and they have to get inside of it. She remembers how the console opened when they were in Cardiff, and they have to get it open so she can make the return trip to the Game Station. When she tells Mickey it has nothing to do with him, he insists that he'll help her.
Daleks approach the human forces and they open fire. Their weapons prove useless and the Daleks quickly dispose of them.
Mickey hooks up a chain from his car to the TARDIS console and tries to pry it open. The chain breaks and Rose kicks the console in frustration.
The Daleks continue their advance and confront the Annedroid. It destroys three of them but a fourth Dalek destroys it. Lynda tracks their progress and realizes that they're going downward. The Daleks arrive on Floor Zero and exterminate Rodrick and other humans. Lynda listens to the slaughter on the intercom and informs Jack of the destruction.
Jackie insists that the Doctor knew what he was doing and wanted to keep Rose safe, but Rose refuses to give up and says that her father Pete wouldn't have given up. When Jackie disagrees, Rose explains that the Doctor took her back in time to meet her father. She describes how the blonde girl who was there and held Pete's hand was her, and Jackie angrily walks away.
Lynda reports to the Doctor that the Dalek fleet has begun the bombardment of Earth.
The Emperor Dalek insists that it has created perfection, Heaven on Earth.
Jack tells the remaining humans to concentrate fire on the eye stalks.
Mickey wonders if there's anything else they can do, and insists that he won't let Rose give up. He suggests they need something bigger... and Jackie arrives with a rescue truck that she's borrowed from a friend. She admits that Rose was right about Pete, and he would have done the same thing.
The Daleks arrive and confront Jack's forces. They open fire and they manage to disable one Dalek's eyestalk. The female programmer is killed and the male programmer dies trying to avenge her. On the top floor, the Daleks detect Lynda and start to cut through the door. She turns around and sees Daleks outside. They open fire on the glass and she is blasted out into space.
Jack retreats to the Doctor's chamber.
Driving the truck, Mickey manages to pry open the TARDIS console. There is a burst of energy that envelops Rose as she looks into the heart of the time vessel. The doors close, sealing Mickey and Jackie outside, and they watch as it dematerializes.
Jack warns the Doctor that he has 20 seconds and tries to hold off the Daleks.
The TARDIS shoots through the Time Vortex as Rose is filled with golden energy.
The Daleks gun down a defiant Jack.
The Doctor finishes the delta wave projector as the Daleks enter the chamber and surround him. He warns them that they will die if he activates the signal, but the Emperor Dalek insists that it is God and will survive. The Doctor considers the trigger... and then refuses. The Emperor Dalek insists that humanity will be harvested, and the Doctor will be killed. he wonders if it's time, and prepares to die. However, the TARDIS materializes nearby and the doors open. A glowing Rose emerges and she explains that she looked into the TARDIS and it looked into her. The Doctor realizes that she has looked into the Time Vortex. The Daleks open fire but their weapons are meaningless. Rose explains that she scattered the words "Bad Wolf" throughout time and space to lead herself to that moment. The Doctor warns her that the vortex is running through her head and she will burn out, but she insists that she wants the Doctor safe. Rose then informs the Emperor Dalek that it is tiny and destroys its forces with a gesture. With another thought, she destroys the Emperor Dalek in its ship.
The Doctor tells Rose to stop, but she insists she must bring life. Elsewhere in the station, Jack comes back to life. She then tells the Doctor that she controls everything, but he warns that the power will kill her. He embraces her and kisses her, and takes the vortex energy into himself. Rose collapses and the Doctor releases the energy,
Elsewhere in the station, Jack considers the dust that is all that is left of the Daleks. He hears the TARDIS dematerializing and runs to the chamber, only to see it leaving without him.
Inside the TARDIS, Rose wakes up and all she remembers is singing. As she talks, the Doctor contemplates his hand, with veins of energy running through it. He explains that they may travel, but it won't be the two of them together because he's going to regenerate because the vortex energy is destroying every cell in his body. Her tells her that she was fantastic, and so was he. His body bursts with energy and his features change.
Seconds later, a new Doctor considers his new body and says that now it's time to go to Barcelona.