Rose is standing on the beach, telling the story of Torchwood, "the last story I'll ever tell."
The Black Dalek leads the other Daleks out of the void ship but Rose identifies them and mentions the Time War, and says they have to keep her alive to find out what she knows. The Daleks are more concerned with the "Genesis Ark," a domed object within the void ship.
As the Cybermen take over the Earth and announce their intent to remove all negative emotions and human distinctions, various soldiers fight back but only heavy artillery is of any use. The Doctor, Yvonne, and Jackie watch the chaos from the Torchwood building and the Time Lord tells the Cyberleader that the humans will never surrender.
The Daleks insist Rose identify the one who is least important and Rajesh volunteers. The Black Dalek tells him to kneel then demand knowledge about human history and extract the information from his brainwaves… killing him in the process. The Cybermen send two of their number to investigate the sphere chamber while the Daleks learn of the Cybermen's operation. The Cybermen squad engages the Dalek scouts and neither side yields. They eventually figure out who their opponents are while the Doctor calls Rose on Jackie's phone and determines she's still alive. He overhears the Daleks speak of the Genesis Ark while the Cybermen propose an alliance. The Daleks refuse and the two sides open fire. The Daleks quickly dispose of the Cybermen and the Cyberleader acknowledges they have a state of war.
The Daleks spot the Doctor with the Cybermen over the broadcast and recognize him as a Time Lord, and determine that Rose is with him. The Cybermen take away Yvonne and Jackie for conversion while the Daleks prepare to activate the Genesis Ark. Rose suspects that they're being kept alive for some purpose.
Yvonne and Jackie are taken to the conversion area in the construction part of the building, where a defiant Yvonne insists she did her duty and steps in for conversion. The Cyberleader points out that the Doctor's emotion will lead to his destruction but they're interrupted when Jake from the parallel universe arrives with a squad of men and makes quick work of the Cybermen guarding the Doctor. Jake quickly explains that they figured out a way to cross dimensions thanks to the work of their version of Torchwood. Jake activates his own and takes the Doctor to his parallel world. He reveals that they found out what Torchwood was up to and put an end to them. Peter Tyler arrives and insists that the Doctor will do what they tell him.
Rose brings Mickey up to speed about how she previously activated a Dalek because of the temporal radiation she absorbed. Since they've both absorbed temporal radiation, the Daleks need one or both of them. The Black Dalek reveals that the Genesis Ark belongs to the Time Lords and is the last surviving relic of their homeworld. The Black Dalek says that the "future" is inside of it.
Peter and Jake explain that they kept the Cybermen alive to find a way to reverse the conversion process, but they managed to infiltrate Torchwood, escape, and disappeared three years ago. Peter explains that Harriet Jones is the new Prime Minister and the weather patterns have been getting worse. The Doctor concludes that all of the dimensional travel is disrupting the weather and both Earths will fall into the void. Peter wants the Doctor to seal the Cybermen away on "his" world. In return the Doctor appeals to Peter with the possibility of being reunited with his parallel-world wife and child, but Peter insists on saving his world and believes the Doctor can do it. The Doctor agrees and they jump back to his world.
Jackie has escaped in the confusion of the Cyberleader's destruction and tells the Doctor where she is. The Doctor modifies Jake's gun to work on Dalek armor and then surrenders to the Cybermen.
The Daleks want Rose to place her hand on the Genesis Ark to activate it and threaten to kill Mickey if she doesn't. She agrees, but then talks about how she knew the Dalek Emperor… and destroyed it. The Daleks prepare to exterminate her… but the Doctor arrives. He realizes the four Daleks are part of the Cult of Skaro and have names. The Cult is a secret order above and beyond the Emperor, tasked with thinking as the enemy thinks. The Doctor doesn't recognize the Genesis Ark but the Daleks say temporal radiation will wake up the contents of the Ark. He reveals his sonic screwdriver and uses it to open the doors into the room. Jake and the Cybermen charge in and open fire while Peter gets Rose to safety and Mickey grabs a gun to add his firepower. The Cybermen start to lose but Mickey inadvertently touches the Ark before escaping, activating it. The Daleks take the now primed Genesis Ark out, saying it needs space.
Jackie is fleeing through the halls when she runs into two Cybermen. They prepare to kill her but Peter arrives with the others and destroys them. The Doctor explains to a shocked Jackie that Peter is from a parallel universe and he explains that he got lucky with his life, and she admits there was never anyone else in her life. He tells her to be proud that she brought up Rose and they embrace.
The Daleks take the Genesis Ark through the building, and the combined forces of the Torchwood soldiers, parallel world troops, and Cybermen are unable to stop them. The new Cyberleader calls back the other units in London to the Torchwood Tower to stop the Daleks. The Doctor and the others emerge into the chaos and the Doctor grabs two magna-clamps, recovered alien technology. The Daleks open the roof access and levitate into the air. The Genesis Ark opens as the Doctor and the others take the lift to the top of the Torchwood Tower. The Ark opens and reveals it's bigger on the inside than the outside… it's a prison ship containing millions of Daleks.
The Cybermen in the streets open fire on the hovering Daleks and a massive war breaks out with humans caught in the crossfire. Peter prepares to return to his world and take Jackie with them. Their world will be safe… as long as the Doctor closes the breech. The Doctor goes to work and points out that the 3-D glasses he's been wearing let him see the void. He explains that anything that has passed through the void will be sucked back into it, so Rose has to go with Peter and the others before he seals the breech for good. He'll use the magna-clamps to anchor himself and avoid being sucked in, but the Daleks and Cybermen will have no such protection.
Rose is reluctant to go but as the building starts to shake, Peter says they must leave. Jackie refuses to leave without Rose until Rose explains she can't leave the Doctor. The Doctor puts the necklace around her and Peter activates them all, and they go back to the parallel universe. Rose reactivates her necklace and goes back to the real world, and Peter refuses to let Jackie go back after her. Rose insists she's made her choice and will never leave the Doctor. The Doctor accepts what she's done and assigns her to help.
The Cybermen approach the top floor but one Cyberman stands against them and guns them down. It's Yvonne, fulfilling her duty to the last. The Daleks sense the Doctor and approach the top floor while he and Rose plant the clamps and activate the breech. The Daleks are sucked into the void and then the other Daleks and Cybermen alike are pulled toward London and into the breech from all across the world. The Black Dalek activates an emergency temporal shift and manages to depart.
One of the Daleks being sucked into the breech knocks the lever down, starting to cut off the breech. It's the lever near Rose, and she has no choice but to let go of the clamp and put the lever back into position. The remaining invaders are sucked into the void, but Rose inevitably loses her grip and is pulled into the void after them as the Doctor can only scream in frustration and anger. But at the last second Peter appears, grabs her, and reactivates the dimension-traveling device. The breech closes… with Rose trapped on the other world.
On the other world, Rose pounds on the wall as Peter notes that their devices no longer work--the breech is closed for good. The Doctor contemplates the wall from his side as well. However, eventually they have no choice but to turn and walk away.
Later Rose is sleeping and reveals she heard the Doctor's voice in a dream. She explains to the others who believe her, and packed up to follow the voice. They eventually arrive in Norway in Bad Wolf Bay. A hologram of the Doctor appears, and he reveals that he's in the TARDIS and has managed to communicate through one brief closing fracture between the universes, using a supernova to power the transmission. He warns that he couldn't physically come through or the fractures would start again, and he only has two minutes
Rose explains that Jackie is pregnant and she is working with the new Torchwood organization on the planet. The Doctor tells Rose that she has been officially declared dead, and now he will be traveling alone, the last of the Time Lords. Rose says she loves him and he starts to say something… but the connection breaks before he can finish. Jackie moves to comfort a sobbing Rose.
Back in the TARDIS, the Doctor cries briefly before moving to the console. But as he prepares to dematerialize, he sees a woman in a wedding dress standing inside. She demands to know who he is and where she is.