The Doctor is still regenerating, and then redirects the energy into his severed hand within the jar in the TARDIS. He falls back, healed but still in his tenth body, leaving Rose, Jack, and Donna utterly confused.
The Daleks prepare to kill Sarah Jane when Mickey Smith and Jackie Tyler teleport in and destroy them with energy rifles. Jackie asks Sarah where Rose is.
Ianto and Gwen are still firing on the Dalek as it invades Torchwood HQ. The bullets stop in mid-air and Gwen determines they're somehow frozen in time, along with the Dalek.
The Doctor checks out his severed hand and explains that once he healed, he redirected the regeneration energy into the hand to avoid losing his current body. He reminds Rose that he lost his hand during his sword fight in the Sycorax invasion. "You're still you," she says as she approaches the Doctor. He confirms it. After two years of being separated, the Doctor and Rose hug each other tightly, overjoyed to be together again.
Ianto determines that their former comrade Tosh complete a time-lock defense system before her death. The Dalek is frozen in the entry, but he and Gwen can't leave. It's up to Jack now.
The Daleks locate the TARDIS in the street and surround it in a temporal prison, causing it to lose power. It is then transported to the Crucible. Sarah Jane, Mickey, and Jackie see it but are unable to intervene. Sarah Jane asks Mickey if they can use their teleports - which are also dimension jumps - but their devices need 30 minutes to recharge. With time running short, Sarah Jane advises them to put down their guns and surrender so that the Daleks will take them and the other human prisoners to the Crucible for testing. She surrenders and Jackie and a reluctant Mickey follow suit.
Martha dons the teleport harness and tells her mother that she has to go. Francine asks about the Osterhagen Key, but Martha says nothing. She tells her mother she loves her and teleports away to Germany, 60 miles outside Nuremberg. Martha narrowly avoids the Daleks in the area.
As the TARDIS is taken to the Crucible, the Doctor asks Rose what happened in her parallel world, which is running ahead of theirs. Rose and Donna mention the coming darkness, as well as the stars going out, which happened in Donna's parallel world. Rose explains that they - the parallel Torchwood - have been building a dimension cannon, which would allow Rose to come back. It started to work, but she realized that the walls of reality were breaking down, even the Void was dead. Something was destroying everything. When Donna's involvement comes up, Rose notes that the dimension cannon can measure timelines, and they all seem to be converging on Donna as the focal point.
They arrive in the Supreme Dalek's chamber and the Doctor orders them all out. Rose and Jack remind him of the TARDIS' defenses. The Doctor notes that, unlike the Daleks they faced in the year 200,100, they are facing a full-fledged Dalek empire at the height of its power, and they're capable of anything. Donna, who starts hearing a heartbeat again, stays behind and the TARDIS doors close on their own. The Doctor demands that the Supreme Dalek release her but it denies any involvement. However, it sends the TARDIS through a tube into the ship's Z-Neutrino drive, noting the TARDIS is a weapon to be destroyed. The Doctor and the others look on in horror as the TARDIS starts to dissolve in the white-hot energy core.
As the TARDIS interior bursts into flames, Donna sees the Doctor's severed hand moving. Touching it, there's an enormous release of energy and the jar shatters. There's a flow of the Doctor's regenerative energy from the hand to Donna and then it regenerates into a copy of the new (and now naked) Doctor. The New Doctor dematerializes the TARDIS so that it appears that it is destroyed in the flames.
The Supreme Dalek taunts the Doctor. An angry Jack pulls out a gun and shoots the Supreme Dalek. It's unaffected and seemingly kills him. Rose, unaware of Jack's abilities, cries over his corpse but the Doctor knows better. As the Doctor and Rose are taken to Davros, Jack winks at the Doctor.
As the New Doctor repairs the TARDIS, keeping it on low power, he explains that when she touched his hand, it instigated a biological meta-crisis. Now he has part of her DNA and starts talking and acting like her, and realizes he has only one heart. He assures her that she's special but when she insists she isn't, he knows what she's thinking through their common DNA and realizes how insecure she is. He starts to put the pieces together in his head. Donna meeting the Doctor in the first place was no coincedence: she materialized in the TARDIS, she parked her car right were the TARDIS landed, and now the meta-crisis. The two of them were always headed for this, but the pattern isn't complete yet.
Martha goes to a castle and confronts a local woman who says that the soldiers guarding the castle abandoned it and died fighting the Daleks. Martha goes in to a hidden elevator but the woman pulls a gun. The local woman knows of the Osterhagen Key and is willing to kill Martha to stop her, but Martha convinces her that they have no choice but to use it. She goes down to a hidden control center and tries to make contact with the other Osterhagen stations.
Two Daleks put Jack's corpse in a disposal bin to be incinerated. After they leave, he slips out and moves through the Crucible ship. While Sarah Jane, Mickey, and Jackie are herded in with the other prisoners, the Doctor and Rose are taken to Davros and confined in holding cells (cylindrical force fields). Davros boasts of his triumph but the Doctor realizes that the Daleks have made their creator a prisoner. Davros says that he has reached an "arrangement" with his creations, then notes that Rose's coming was foretold by Dalek Caan. Caan is present and speaks of how in the near future the Doctor and his "Children of Time" will be there to witness the end of everything. Further, one of the Doctor's "Children" will die, and the Doctor's true soul will be revealed. Satisfied, Davros says that they are ready to test the Reality Bomb.
Sarah Jane and Mickey manage to slip away from the other prisoners as they're herded into a test chamber. Jackie falls behind to help a frightened woman and is unable to escape. The Supreme Dalek orders the test to begin and the Reality Bomb overhead starts to activate as the Daleks draw on the power of the 27-planet configuration. The Z-neutrino stream tightens into a single strand. Both Doctors realize what's about to happen and are both shocked. Mickey's teleport device goes off. It's recharged and gestures to Jackie to use hers. She apologizes to the prisoners and then teleports out to the others. The Reality Bomb "detonates" and the human prisoners disintegrate into dust. Davros boasts that the Reality Bomb negates the electrical energy of atoms, which is what binds all living things together. He and the Daleks can destroy every other life form in all of the universes by using the power of the planetary configuration to send a destruction wave through all the dimensions via the Medusa Cascade.
The Daleks withdraw to the Crucible for protection against the wave, and the citizens of Earth start to celebrate. Wilfred realizes that it's not over yet, however. Jack, using his wrist device, finds Sarah Jane, Mickey, and Jackie, and they have a brief reunion. Sarah Jane shows him a necklace that a seer gave her: a warp star, containing an enormous explosion in stasis. Jack has just been given a bargaining chip.
Martha contacts two other UNIT officers at separate Osterhagen stations. Despite their knowledge of what is involved, they feel they have no choice but to proceed. However, Martha hesitates. She answers to an authority "way above UNIT," and she knows what the Doctor would do next.
Aboard the TARDIS, the New Doctor is creating a weapon that will lock the Crucible's transmission onto Davros, which would destroy the Daleks since they are made out of his DNA.
Martha contacts the Dalek fleet and calls upon them to surrender. She explains that the Osterhagen Key triggers 25 hidden nuclear warheads, capable of destroying the Earth as a final option. The Doctor is shocked that Martha would even consider this. She concludes that with one planet destroyed, the Daleks' will be unable to use the Reality Bomb. Rose comments on this, and Martha asks who she is. For a moment, Martha is stunned that it's Rose.
Jack transmits from his location and says he's wired the warp star into the mainframe: they can destroy themselves and everyone aboard. Sarah Jane steps forward admitting that she gave him the warp star. Davros is stunned at Sarah Jane's appearance, remembering that she was on Skaro at the creation of the Daleks. Caan's prophecies are all coming true as the circle of time closes back upon itself. Turning to the Doctor, Davros boasts that the Time Lord's "true soul" has been revealed: he turns his Children of Time into murderers.
The Supreme Dalek, unimpressed, teleports Martha, Jack, and the others into Davros' vault. As per Caan's prophecies, all of the Children of Time are together with the Doctor and Davros prepares to complete the prophecy. He commands the Supreme Dalek to detonate the Reality Bomb, boasting that no one can stop them. However, the New Doctor brings the TARDIS to full power and materializes it into the Vault. The New Doctor steps out. He tries to use the DNA weapon but Davros blasts him with a lightning bolt and then imprisons the New Doctor in another holding cell. Donna tries to get to the weapon but Davros shocks her as well. On Davros' orders, the weapon is destroyed.
Everyone looks on in horror as the countdown reaches zeroÃ¢â'¬Â¦ and power drops all over the ship. Donna is at a control panel and boasts that she has shut down the power. When Davros and the Daleks try to open fire on her, she negates their weaponry and then explains that she has enhanced intelligence because she has the Doctor's intelligence: it was a two-way meta-crisis. It was dormant until Davros shocked her. The New Doctor gained some of her DNA and she gained some of the Doctor's. She frees everyone and scrambles the Daleks' gyroscopic controls, rendering them harmless. Jack gets the energy weapons from the TARDIS. He and Mickey take Davros prisoner while Donna and the two Doctors use the controls to send the planets back to their proper time and space. Davros demands to know why Caan didn't warn him of this defeat, but the Doctor realizes what's happened: Caan did foresee it, and manipulated the timelines to put Donna in the right place at the right time. Caan confirms his theory, stating that this would always have happened, but he helped. After he shifted into the Time War, he was able to see everything the Daleks have done throughout time and space. Caan saw the truth of them, and now he has decreed, "No more."
The Supreme Dalek descends into the vault and opens fire on the Doctors. It misses, but it destroys the control panel before they can return the Earth. Jack destroys it and the Doctor goes into the TARDIS so they can return the Earth. Caan tells the New Doctor that he must assure the Daleks' destruction, since their fleet is still powerful enough to destroy the universe even without the Reality Bomb. The New Doctor triggers a Dalekenium backlash, destroying all of the Daleks in the fleet. As the ships go up in flames, the Doctor emerges and realizes what has happened. Angry at the genocide, he gets everyone into the TARDIS and then tries to get Davros to safety. Davros refuses, naming the Doctor the "Destroyer of Worlds." He's engulfed in flames, while Caan warns that "one will still die" before being killed by falling debris.
Everyone escapes in the TARDIS but Earth is still in the wrong part of space. The Doctor contacts Torchwood and has them open the Cardiff rift and direct the power to the TARDIS. He asks if Gwen comes from an old Cardiff family. She confirms that her family goes back to the 1800's. The Doctor and Rose realize that they met one of Gwen's ancestors in the year 1869. He then contacts Luke and Mr. Smith and has the super-computer loop the energy around the TARDIS. Mr. Smith needs the TARDIS base codes but it would take too long to enter manually. Sarah Jane summons K-9 from his mission and has it enter the information. The Doctor then has five of his companions man the TARDIS console, explaining it was originally designed to be piloted by six people simultaneously. They focus the power of the rift into a giant energy towrope, snag the Earth, and tow it back to its proper position.
People celebrate worldwide while the Doctor bids goodbye to his companions. Sarah Jane leaves while Donna calls her family and Mickey says goodbye to Jackie. Jack and Martha depart next, after the Doctor disables Jack's wrist teleporter a second time. Jack hints that Martha should be working for Torchwood. Mickey steps out, having decided to stay in his universe. His grandmother has died peacefully, and adds that there's nothing left for him in the parallel world. He goes to catch up with Jack and Martha.
The Doctor then takes his counterpart, Jackie, Rose, and Donna to Bad Wolf Bay in the parallel universe. The rift is closing again after the destruction of the Reality Bomb and the Doctor asks Rose to stay there. They saved the universe, but at a cost. The New Doctor had committed genocide, and he's too dangerous to be left on his own. He was born in battle, full of blood, anger, and vengeance. His predecessor, the Ninth Doctor, was the same way when he first met Rose, and now he needs her to help make him better. Rose thinks that the New Doctor isn't the real Doctor, but Donna states what the Doctor is trying to give her. The New Doctor looks and thinks just like his counterpart, but he has one heart and will age normally: they can be together and grow old together. Rose asks them both what the Doctor said the last time they were at Bad Wolf Bay. The Doctor says it doesn't need to be said, but the New Doctor whispers the same words in her earÃ¢â'¬Â¦ and then kisses her. The Doctor and Donna leave in the TARDIS as the New Doctor and Rose watch on, hand-in-hand.
The Doctor and Donna go back through the rift and Donna starts planning a trip across the universe. However, she starts to overload from all the information in her mind. They both know why. She can't handle a Time Lord's mind. The reason why there's never been a meta-crisis is because there can't be. Donna realizes what he intends to do to save her and begs him not too, but he touches her head and strips her of all of her memories of their time together.
The Doctor returns Donna home and tells Wilfred and Sylvia what happened. He explains that if she ever remembers what happened, the knowledge will return and burn her up in a matter of seconds. Sylvia and Wilfred will have to lie to her, and convince her that the transportation of Earth was just another alien invasion she missed. The Doctor explains that Donna was important, saving the lives of billions of people. Sylvia says that Donna, her daughter, still is important, and the Doctor reminds her she should say that to Donna sometime. Donna comes down from her bedroom and doesn't recognize the Doctor, who introduces himself as John Smith.
Donna goes to call her friends while Sylvia tells the Doctor it's time for him to leave. As he goes, he waves goodbye to Donna who is busy chatting on the phone. Wilfred escorts him to the door and wonders who the Doctor has now. The Doctor says he doesn't need anyone, and Wilfred promises to look up to the sky from time to time to keep an eye on him, for Donna's benefit. The Doctor thanks him and then leavesÃ¢â'¬Â¦ alone.