The Doctor glows with the energy of regeneration… and directs it into his severed hand, sitting in a jar. He staggers back, still in his tenth body.
The two Daleks prepare to open fire on Sarah Jane Smith, but Mickey Smith and Jackie Tyler dimension-jump in and destroy them with their weaponry. Jackie demands to know where Rose is.
At Torchwood HQ, Ianto and Gwen open fire on the invading Daleks, only to stop when they notice the bullets stopping mid-air, frozen in some kind of force field.
The Doctor examines his severed hand as it stops glowing. he then explains that he used the regenerative energy to heal but then siphoned it off into his hand to avoid complete regeneration. Rose hugs him.
Ianto realizes that Tosh completed the time-lock, and the Dalek is frozen in stasis but they’re trapped inside Torchwood HQ.
The Daleks find the TARDIS, lock it in a temporal prison, and beam it to the Supreme Dalek at the Crucible. Sarah Jane, Mickey, and Jackie look on and Mickey explains their teleportation device takes a half hour to recharge before they can go to the Crucible. Sarah Jane advises Mickey and Jackie to put their guns down, and then they all surrender so the Daleks will take them to the Crucible.
Martha puts the teleport back on and tells her mother that she loves her, then departs with the Osterhagen Key. She arrives in Germany, 60 miles outside of Nuremberg, as Daleks patrol the area.
As the TARDIS is drawn to the Crucible, Rose explains that in her parallel world which runs ahead of the Doctor’s, the Daleks built a dimensional cannon and start collapsing the dimensions. She notes that all of the timelines seemed to converge on Donna. They arrive and the Daleks order them out. The Doctor realizes that the Daleks can breach the TARDIS and prepares to leave, but Donna seems paralyzed, the sound of a heartbeat in her ears. The Doctor snaps her out of it and they go outside… but Donna remains behind and the TARDIS doors close on their own. The Supreme Dalek denies doing anything, but jettison the TARDIS down a tube to destroy it in the Crucible’s neutrino power core.
The TARDIS starts to destruct and the Doctor is forced to watch. He begs the Daleks to save her while inside, Donna sees the Doctor’s hand. She touches it and regenerative energy flows into her as the jar shatters. The hand twitches on the floor and then regenerates into a new, naked Doctor. He dematerializes the TARDIS just as it should disintegrate, and the Daleks believe it destroyed.
The Supreme Dalek mocks the Doctor’s emotions, and Jack opens fire on it with a pistol. It’s unaffected and exterminates Jack, then sends the Doctor and Rose to Davros. The Doctor, aware of Jack’s immortality, sees Jack wink at him as they’re taken away.
The New Doctor repairs the TARDIS systems and then explains to Donna that he regenerated thanks to her touching the hand, and he has human DNA: her DNA. He starts to act like her and realizes that he only has one heart. The New Doctor explains that she heard his single heartbeat because of a ripple in time and space, and that she’s special. Attuned to her thoughts through their shared DNA, he realizes that she feels insecure. However, the New Doctor realizes that something has brought them together, but the pattern isn’t complete yet.
Martha finds the castle she’s looking forward, and a local woman who informs her that the soldiers guarding left to fight the Daleks. Martha goes inside and activates a security vault, but the local woman says she knows of the Osterhagen Key. Martha refuses to surrender and the woman yields.
The Daleks dispose of Jack’s body and after they leave, Jack slips out. Meanwhile, Martha enters the security vault and activates Osterhagen Station One, attempting to make contact with the others.
Sarah Jane, Jackie, and Martha are escorted through the Crucible while the Doctor and Rose are taken to Davros and confined in holding cells. The Doctor realizes that Davros is a prisoner of the Daleks, not their commander. In turn Davros knows that Rose’s coming was foretold by Dalek Caan, who is present. Dalek Caan knows the future, and says that the Doctor and his “Children of Time” will witness the end of everything… and one of them will die. It also notes that the Doctor’s true soul will be revealed at the end of things. Davros says they’ll find out together, and says that the testing of the Reality Bomb is to begin.
Sarah Jane and the others are escorted with the other prisoners. When a woman stumbles, Jackie goes to her aid and Mickey and Sarah Jane slip away during the distraction. However, they have no choice but to leave Jackie behind as they watch through a porthole. The Reality Bomb overhead begins to glow and the Daleks activate the planetary alignment field. All 27 planets swing into alignment and the neutrino stream compresses into a single strand.
In the prison hold, Mickey realizes that the dimension jump devices have recharged and he signals Jackie. She has no choice but to use hers to teleport out to Mickey and Sarah Jane. They look on as the human prisoners are separated into their component atoms. Davros explains that the Reality Bomb negates the electrical binding field of atoms, and using the 27 planets he can transmit the wave across the universe that will destroy all matter, in every dimension.
The Dalek retreats to the protection of the Crucible, and Sylvia thinks they have left for good. Wilfred warns her that it’s not over yet. On board the Crucible, Jack finds Mickey and the others, and Sarah Jane reveals she has a necklace given to her by a soothsayer who said it was for the “End of Days.” It’s a trapped warpstar: an explosion waiting to happen.
Martha makes contact with two other Osterhagen stations and none of them are reluctant to proceed. Martha says there’s one more thing that the Doctor would do. Meanwhile, aboard the TARDIS the new Doctor is creating a device to lock the Crucible’s wavelength on the Davros’ genetic code… and he created the Davros from his own DNA.
Martha contacts the Dalek fleet and Davros lets the Doctor speak with her. She informs everyone that the Osterhagen Key triggers 25 buried nuclear warheads, destroying the Earth. With Earth’s destruction the Daleks’ planetary configuration is shattered. Jack chimes in on another frequency, saying he’s wired the warpstar into the ship’s drives and will activate it. Davros recognizes Sarah Jane from the creation of the Daleks and believe the circle of time is closing back upon itself. He gloats, saying that he has forced the Doctor to show his true self: a creator of human murderers.
The Supreme Dalek has its minions activate the transmat, beaming everyone to Davros’ chamber before they can activate their destruct systems. Davros believes that the prophecy has been fulfilled and the Doctor and his “children” will serve as witnesses. He orders the Supreme Dalek to activate the Reality Bomb and laughs in triumph, yelling that no one can stop them.
The New Doctor materializes the TARDIS in Davros’ chamber, then charges the Daleks’ creator. Davros fires a lightning bolt at him, causing him to drop his genetic device, and then imprisons him in a holding cell. Donna grabs the device but doesn’t know how to activate it, and Davros throws her back as well. A Dalek destroys the weapon and the countdown reaches zero… and everything has shut down. Donna, unobserved, has negated the power. She negates Davros and the Daleks’ weaponry and explains that the regenerative energy transfer was two-way: she’s now part-Time Lord. She deactivates the holding cells and the two Doctors go to work, while she scrambles the circuits of Daleks across the ship. Working together, the three of them send the planets back to their original time and space. Donna explains when Davros electrified her, it triggered the dormant synapses in her brain, letting her access the Time Lord DNA.
Mickey and Captain Jack hold Davros at bay, and the Daleks’ creator asks Dalek Caan why it didn’t foresee what happened. The Doctor realizes that Caan has been the one manipulating the time lines to bring him and Donna together. Caan explains that it saw the truth of the Daleks and it decreed no more. The Supreme Dalek enters the vault and opens fire, destroying the planet-shifting device before Earth can be restored. Jack destroys it and the Doctor goes into the TARDIS to use its controls.
Dalek Caan informs the Doctor that he must assure that the Daleks are destroyed. The New Doctor realizes that the Dalek fleet is still powerful enough to destroy the universe through conquest, and causes a Dalekenium backlash to destroy the Daleks. The Doctor, angry, gets everyone into the TARDIS and goes back for Davros. The Daleks’ creator refuses to go with him and names the Doctor the Destroyer of Worlds. Flames engulf him while Dalek Caan warns that one will still die.
The TARDIS dematerializes as the Crucible explodes. The Doctor contacts Ianto and Gwen at Torchwood and has them open the rift and direct the power to the TARDIS. He then contacts Luke and Mr. Smith. The Mr. Smith computer needs the TARDIS computer basecodes and Sarah Jane summons K-9 to provide the information. He then explains that the hexagon console is designed to be operated by six people simultaneously and has everyone (but Jackie) man the stations. Using the Torchwood rift, they create a giant tow rope and haul the TARDIS back to its proper position.
As people across the world celebrate, the TARDIS materializes and the Doctor drops Sarah Jane off. Donna calls her mother and grandfather while Mickey says he’ll miss Jackie. The Doctor disables Jack’s wrist-teleporter (again) and suggests that Martha get rid of the Osterhagen Key. Jack and Martha depart as Jack suggests that Torchwood might be recruiting. Mickey, back in his home dimension, goes after them.
The Doctor then takes everyone remaining to Bad Wolf Bay in the parallel universe. They have only a limited time before the rift closes again. Rose doesn’t want to stay there, but the Doctor informs her that she has to stay there to guard the New Doctor. He committed genocide, an act of vengeance, and Rose needs to help him to become better. The New Doctor points out that he’s just like the “real” Doctor, but has only one heart and will age normally: he and Rose can be together. Rose asks both of them what they said to her on the beach the last time. The Doctor says it doesn’t need to be said, while the New Doctor whispers it in her ear… and they kiss.
Returning to Earth, Donna starts planning a new tour and the Doctor asks her how it feels. Donna is enthusiastic but she starts to literally overload from all of the Time Lord consciousness in her mind. She realizes what has to happen but had planned to be with him for the rest of her life. She refuses to go back to normal, but he takes her head in his hands and takes away all of her memories of their time together.
Wilfred and Sylvia are at home when there’s a knock on the door. He finds the Doctor holding an unconscious Donna. They take her to bed and then the Doctor explains to Sylvia and Wilfred that if Donna remembers for even a moment, she’ll burn up and die. Wilfred asserts that Donna was better with the Doctor, over Sylvia’s objections. The Doctor assures them that billions of people can live safe thanks to Donna. When Sylvia asserts that Donna is still important, the Doctor suggests she say that to Donna occasionally.
Donna comes in, unaware of anything wrong, and the Doctor introduces himself briefly as Dr. John Smith. She departs to find out from her friends what she missed, while Sylvia tells the Doctor to leave. Wilfred escorts the Doctor out and asks who the Doctor has. The Doctor says he’ll be fine, but Wilfred promises to look up at the sky on Donna’s behalf and think of him.
The Doctor departs alone, in the TARDIS.