Following on immediately from the end of "The Stolen Earth", The Doctor is regenerating inside the TARDIS while Donna Noble, Captain Jack Harkness and Rose Tyler watch in horror. However, the Doctor transfers his regenerative energy into the container which carries his severed hand. He has healed himself, but chosen not to change his appearance. The TARDIS is transported by the Daleks to the Crucible and rendered powerless. The Doctor, Jack, and Rose leave it, but Donna is distracted because she is hearing the sound of a heartbeat and while looking back, the TARDIS door slams closed. Before the Doctor can free her, the Daleks dump the TARDIS into a waste shoot where it will be destroyed in the centre-core of the Crucible. As the TARDIS interior explodes around her, Donna collapses near the severed hand, she hears the heartbeat again and while touching the container energy flows between it and her. The hand bursts out of the container, and forms as a new Doctor, although this Doctor has only one heart and has picked up some of Donna's mannerisms. With his help, the TARDIS escapes destruction and gives the new Doctor and Donna time to come with a plan.
In Torchwood Three, Gwen Cooper and Ianto Jones find themselves safely in a time lock created by Toshiko Sato, preventing the Dalek from entering but also preventing them leaving. Sarah Jane Smith is saved from two Daleks by Mickey Smith and Jackie Tyler, but in order to follow the Doctor, lay down their guns and allow themselves to be captured, taken to the Crucible. Martha Jones says her goodbyes to her mother and makes for an abandoned castle in Germany where one of five Osterhagen stations is hidden, and waits for contact from the other bases.
Aboard the Crucible, Jack creates a distraction by shooting the Supreme Dalek (Red Dalek) with his revolver, but is shot by the Daleks; as the Doctor and Rose are taken to the Vault where Davros is held, Jack's immortality allows him to escape. With the Doctor and Rose contained, Davros explains that the 27 planets form an energy pattern that is then amplified into a "reality bomb", able to break apart the forces holding everything together. Mickey, Jackie, and Sarah Jane escape a test chamber where this effect is shown to the Doctor just in time. Jack finds his way to the three, and with a locket from Sarah Jane, creates a device that will implode the Crucible. Meanwhile, Martha makes contact with two other bases in China and Liberia. The Chinese counterpart wants to get it over and done with, but Martha, knowing the Doctor, first broadcasts a signal to the Crucible to give them (probably both Earth and the Daleks) a second chance, promising to use the Ostenhagen key to detonate 25 nuclear warheads under the Earth's crust to destroy it and disable the reality bomb. However, the Daleks manage to lock onto their positions and beam Martha, Jack, Mickey, Jackie, and Sarah Jane, with the Transmat to the Vault where the Doctor and Rose are too being held captive.
The Daleks prepare to activate the reality bomb that will wipe out all matter in this and every parallel universe through the rifts in the Medusa Cascade, but the new Doctor and Donna arrive in the TARDIS. Both, however, are stunned by shots from Davros. The reality bomb countdown reaches zero, but nothing happens; Donna has manipulated the controls to disable it. The Doctor recognises that the creation of the new Doctor has had an unintended side effect: Donna is now half Time Lord herself, sharing the Doctor's intellect. Donna and the new Doctor free the others, and with the help of the original Doctor, disable the Daleks and start to send the planets back to their proper time and space. Before Earth can be sent, the machinery is destroyed, and the original Doctor races into the TARDIS to replace the functionality of the broken machine. Realising that Dalek Caan has seen the end of the Dalek race and has been manipulating time to achieve this, the new Doctor (probably not kept back by guilt due to the influence of Donna's personality) uses the remaining machinery to destroy all of the Daleks and their fleet. The rest of the companions flee to the TARDIS, and while the Doctor offers to save Davros, but he refuses, calling the Doctor the "Destroyer of Worlds". The Crucible is destroyed.
The Doctor enlists the help of the other companions, making contact with the base Torchwood and with Luke Smith, Mr. Smith and K-9, to help use the TARDIS return the Earth to its proper place. Sarah Jane says her goodbyes, as well as Jack, Martha, and Mickey, who has decided to stay in this universe. Using a retroactively closing rift, the Doctor returns Rose and Jackie to the alternate dimension and leaves the new Doctor with her, as he will now grow old with Rose, no longer able to regenerate due to the human influence, the human doctor, having the same memories and feeling as the proper Doctor tells Rose he loves her and they kiss.
Returning to their universe, Donna finds she begins to have trouble thinking; the Doctor explains that the human mind cannot take in the Time Lord mental abilities. To save her, he wipes her mind of all her encounters with the Doctor, returning her home and explaining to her family, Sylvia Noble and Wilfred Mott, that she must never be reminded of her time with the Doctor or else she will die. As Donna recovers consciousness, she shows no interest in the Doctor; he leaves, though Wilfred promises that he will remember the Doctor whenever he looks into the sky.