On board the Dalek ship, the Daleks demand that Rose predicts what The Doctor will do next, but she can't answer. The Daleks detect the TARDIS and launch missiles at it. However, thanks to some modifications made by Jack, the TARDIS now has a fully functional force field and is undamaged.
The TARDIS enters the Dalek ship where Rose is being held prisoner, cleverly landing where Rose is standing and bringing her inside. Unfortunately, a Dalek also enters the TARDIS. Jack shoots and destroys it almost immediately.
Protected by the TARDIS' force field, they are able to leave the TARDIS safely to speak to the Daleks. The Doctor tells them that even though they have no human emotion, he's sure that they are still afraid of him. He then asks how they survived the Time War and a deep voice says:
"They survived through me."
The Doctor turns around and discovers that it was the Emperor Dalek who had spoken.
The Emperor Dalek says that he survived the Time War and has been slowly re-building the Dalek race over centuries from the bodies of humans. He claims that since he created them, he is now the God of the Daleks, prompting the Daleks to go into a chorus of:
"Worship him, worship him"
The Doctor says that humanity has made Daleks hate their own existence "and that makes them more deadly than ever." The Doctor, Rose and Jack leave the Dalek ship and return to the Game Station, which has been partially evacuated. There are still a few members of staff that have remained behind, as well as Lynda and about a hundred people on floor zero. The Doctor realizes that he can transmit a delta wave from the Game Station which will kill all of the Daleks, but he doesn't know if he can create it before they invade the Game Station and Earth.
Jack creates a force field around the Game Station to stop the Daleks from destroying it, concentrating the field around the highest floors so that when they do invade, they'll have to start off at the 494th floor and it will take them longer to get to The Doctor He also recruits the remaining members of staff to help him defend the Game Station and Lynda to help him track the Daleks. Sure that he won't survive the upcoming fight, Jack says to The Doctor and Rose:
"It's been fun, but I guess this is goodbye."
He then kisses them both goodbye, genuinely happy to have known them.
Down on Floor Zero, Jack attempts to recruit some of the people left on the Game Station to help him defend it, but most believe that they're not in any danger and don't join him.
Back on Floor 500, the delta wave begins to build and The Doctor tells Rose to go into the TARDIS, but he doesn't tell her why. As soon as she's inside, he uses a device he has to start the TARDIS up and it disappears.
In the TARDIS, a hologram of the Doctor appears with a message for Rose. It tells her that since the message has been activated, they must have been in danger and that The Doctor was either "dead or about to die at any second, with no chance of escape."
The hologram of The Doctor continues to tell her that he's sending her home and it can never return for him. Lastly, the hologram turns to face Rose directly and says:
"Have a good life. Do that for me, Rose. Have a fantastic life"
The hologram then disappears and the TARDIS stops. Rose gets out to see that she is in London. Home. Mickey, having heard the TARDIS runs to meet her and Rose begins to cry for what she has left behind. Later, while in a café with her mother and Mickey, Rose is still upset and frustrated that she can't help The Doctor. Jackie tries to convince her that The Doctor did the right thing by sending her home, but that doesn't make Rose feel any better.
Back on the Game Station, the Emperor Dalek communicates to The Doctor by view screen, saying that he knows what The Doctor is planning. He also says that he knows that the delta wave will wipe out all life on Earth as well as the Daleks. The Doctor asks the Emperor Dalek the meaning of the words 'Bad Wolf' and discovers that the Emperor Dalek was not responsible for it.
Back in London, Rose and Mickey discover the words 'Bad Wolf' written in huge writing across a car park and Rose realizes that the words are a message and that she can return to The Doctor. When she gets back to the TARDIS, she decides that to get back, she needs to open the console and look into the heart of the TARDIS. The TARDIS will then take her where she wants to go. But first she needs to get it open. She and Mickey attach it to Mickey's car to try and pull it open, but it won't budge. Jackie tells Rose that she should give up and Rose replies:
"Dad wouldn't give up"
She tells Jackie that she went back in time and saw her father and that she was with him when he died.
Meanwhile, the Daleks begin invading the Game Station, exterminating everyone that gets in their way. They even go down to floor zero to kill all of the people there. Lynda, who is keeping track of the Daleks, informs The Doctor and Jack that the Dalek fleet has descended on Earth, destroying everything. Soon after, Lynda sees Daleks hovering out in space right next to the window. They shoot through the window, killing her.
As they make their way up towards the 500th floor, the Daleks continue to kill people until Jack is left alone to stop them from getting to The Doctor. He shoots continuously until he is out of ammunition and throws his gun away. The Daleks say:
And Jack replies:
"I kinda figured that"
Knowing that there is no more he can do, he just stands there and allows them to shoot and kill him.
Back in London, Jackie arrives with a truck to help Rose open the console. She tells Rose that she was right about her father – that he wouldn't have given up. They attach the truck to the console and start pulling. After a lot of effort it does finally open. Rose looks into the heart of the TARDIS. Golden energy from inside flows into her, the door closes and the TARDIS leaves.
On the Game Station, The Doctor is now surrounded by Daleks. The Emperor Dalek tells him that if he emits the delta wave, he will be responsible for destroying the human race and asks him if he is a coward or a killer. The Doctor smiles, knowing that he can't kill everyone, he says:
"Coward. Any day."
Just as the Daleks are about to exterminate The Doctor, the TARDIS arrives and Rose steps out of it. Rose, who has absorbed the Time Vortex, says that she is responsible for scattering the words 'Bad Wolf' through time and space, as a message to lead herself back to The Doctor.
With seemingly unlimited power, she disintegrates the Daleks atom by atom, leaving nothing but dust. She then destroys the ship where the Emperor Dalek is and even brings Jack back to life. However, she can't control this power and can't continue to live with the Time Vortex flowing through her.
Unwilling to see her suffer, The Doctor kisses Rose, transferring the Time Vortex into his own body and then back into the TARDIS where it belonged. However, the vortex has already done too much harm to his body.
The Doctor and Rose (who has lost consciousness since the Time Vortex left her) leave in the TARDIS, unaware that Jack is still alive and they are leaving him behind.
Rose wakes up on the TARDIS with no memory of what had happened and The Doctor explains to her that he absorbed the energy of the Time Vortex and that every cell in his body is dying. He explains that Time Lords have a way of cheating death, but it means that he's going to change. The Doctor tells Rose:
"Before I go, I just want to tell you – you were fantastic. Absolutely fantastic. And you know what? So was I."
He then regenerates into a new body.