Rose surprises the Daleks with the fact that she knows about them, telling them that she, Mickey and Rajesh know all about them and the Time War, leading the black Dalek to decide that they will be "necessary" and must not be exterminated. The black Dalek asks the status of the strange device, the "Genesis Ark". It orders the awakening of the contents of the Ark and that it must be protected at all costs. Upstairs, surrounded by Cybermen, Jackie asks the Doctor what was in the Sphere and what has happened to Rose. He promises to get her and Rose out of Torchwood alive. The Cyberleader then broadcasts on all wavelengths to the people of the world. He informs humanity not to fear, as they will be "upgraded", removing fear as well as sex, colour, creed and class.
The Cybermen invasion is met with military resistance, and the Cyberleader does not understand why humanity has not either acknowledged Cybermen as superior or embraced the prospect of becoming like them, and why they resist. The Doctor snaps that they are obviously going to meet resistance, as the Cybermen are in every street and home. Back in the Sphere room, the Black Dalek demands that the humans indicate who is the least important of them. Rose initially refuses, but Rajesh volunteers himself. He is ordered to kneel so they can learn about current Earth history. He says he'll tell them what they want to know, but instead they extract his brainwaves using their manipulator arms. He screams as they crush his skull. The Cyber-Leader has detected alien technology in the "sphere chamber" and sends two Cybermen down to investigate. At the same time, as Singh's burned-out corpse collapses to the floor, the black Dalek has obtained the information about a second species invading Earth. It, too, sends one of the Daleks, which it calls "Dalek Thay", to investigate. Both groups are feeding video information back to their respective leaders, and so the Doctor sees the Dalek as it encounters the two Cybermen.
Each side demands that the other identify itself, and the Dalek lets slip its identity when it proclaims that Daleks do not take orders. The black Dalek also notes that the steel cyborgs bear some resemblance to the "inferior species" known as Cybermen. The Doctor surreptitiously calls Rose using Jackie's mobile phone, confirming that she is still alive when she answers the call. Rose does not speak but keeps the line open, allowing the Doctor to listen in as the Daleks mention the Genesis Ark. The Cybermen propose an alliance to the Daleks: together they could upgrade the universe, but the Daleks refuse. Declaring that "hostile elements will be deleted," the Cybermen open fire on Thay, but their beams simply bounce off its force field. Thay fires in turn, exterminating the two before him. The Cyber-Leader speaks directly to the black Dalek, accusing him of declaring war. Both sides continue to taunt each other, boasting of their military might. As the black Dalek cuts off the transmission, however, he sees the image of the Doctor in the background, identifying him as an enemy. The Daleks turn to Rose, demanding that she identify him. Rose does so, noting with satisfaction that while the Daleks are confident of taking on five million Cybermen, the thought of one Doctor frightens them more.
Requiring more troops in order to fight the Daleks, the Cyberleader orders that Jackie and Yvonne be taken to be upgraded. They are, and Yvonne responds tearfully to Jackie's blame by saying she was only trying to do her duty. She is then converted before Jackie's eyes. Upstairs, the Cyberleader tells the Doctor that he is proof that emotions are self-destructive, and seconds later, a group of soldiers materialise in the middle of the office floor and they fire on the Cybermen with energy weapons. Their leader destroys the Cyberleader, and reveals himself to be Jake, Mickey's comrade from the parallel universe. Downstairs, the Cybermen sense that their leader has been killed and download new information on rankings. This offers Jackie the chance to escape onto the stairwell. The Doctor is surprised to see Jake, and asks him how he got there. Jake responds by throwing him a panel with a large yellow button on it and telling him about the alternate Torchwood. He presses the button, transporting the two of them to the Cybus Earth before the Doctor can stop him. Once in the parallel Torchwood Tower, Pete Tyler steps out of the shadows and tells the Doctor that they're in trouble, and that it's the Doctor's turn to listen.
Rose and Mickey talk downstairs about why they are needed. She tells Mickey about how her touch regenerated a Dalek the first time she met one because she was a time-traveller, and perhaps this is why she and Mickey are needed; they have both travelled in time. The black Dalek overhears and tells them that the Genesis Ark is a piece of Time Lord technology that must be activated because it is "the future". The Doctor and Pete argue in the other universe about how continual crossing between universes makes the breach bigger, and both worlds will boil and fall into the Void if it continues. Eventually, the Doctor agrees to help, but not at the cost of abandoning his own universe to the Daleks and Cybermen. They cross back, and the Doctor calls a truce with the Cybermen, offering "a very good idea". The black Dalek demands that Rose activates the Genesis Ark, just as the Doctor enters the Sphere room. The Daleks and the Doctor exchange words for a while, and it is revealed that these Daleks are part of a group called the Cult of Skaro. The Cult's purpose was to think as the enemy thinks, to find new ways of killing, including daring to take on individual identities. They escaped the Time War in a Void Ship, taking with them the Genesis Ark. Throughout this scene, as throughout the whole two part story, the Doctor puts on 3D glasses every now and then and surveys things.
The black Dalek eventually declares that the Doctor is to open the Genesis Ark, a claim that he laughs off and then gives the signal to the Cybermen and parallel universe soldiers to burst in. Their guns have been modified to work on the skin of a Dalek, but it's still ineffective. As the humans slip out of the room to escape, Mickey falls and puts his hand on the Genesis Ark before escaping. Pete blasts two Cybermen that were about to grab Jackie, and the couple (divided by the Void) are reunited. As the battle rages on between Daleks and Cybermen, the Doctor sneaks into the Torchwood hangar, dodging the crossfire, in order to grab the two magnetic clamps seen in the previous episode. The black Dalek moves into the air and outside the building with the Genesis Ark, and the Doctor follows it to the top floor of the building to see what it's doing, still not knowing what the Time Lord technology is. As they reach the window, the Genesis Ark opens, and starts shooting out Daleks in all directions. The Doctor now realises it's Time Lord science, and so it's a prison ship- bigger on the inside than on the outside.
As millions of Daleks descend on Earth, Pete declares the situation hopeless and tells everyone to go to the other universe and close the breach. The Doctor disagrees as he puts on his 3D glasses and looks out of the window. He explains that the glasses allow him to see the harmless background radiation around things that have travelled from one universe to another, and all the Daleks and Cybermen are steeped in it. His plan is to reverse the ghost shift, sucking everything that has been through the Void back into it before closing the breach. The Doctor tells Rose to go with Pete and the others back to the parallel universe, even though it means she'll never see him again. She refuses and although he sends her anyway, she comes straight back, and Pete refuses to let anyone go back for her. The Doctor and Rose then set up the ghost shift and put the clamps on the wall to prevent them from being pulled into the Void as well. The Cybermen head for the office floor to stop them, but they are met by a Cyberman carrying a large gun levelled at them. They question it before it opens fire. It says "I did my duty for Queen and country" and we realise that this is Yvonne in Cybernised form.
The Daleks and Cybermen are all sucked into the Void screaming, except for the black Dalek, which vanishes in an "emergency temporal shift." Halfway through, one of the huge levers nearest to Rose is partially opened, risking the cancellation of the process. Rose lets go of her clamp to put the lever upright. The shift is put back online and the lever is locked, but Rose is left clinging for dear life to the lever as the Void tries to consume her. She can't hold on, and she lets go, flying hopelessly towards oblivion. The Doctor screams in anguish, but right at the last minute, Pete materialises in front of the breach and grabs her before quickly crossing back. The Doctor looks relieved that she's alive, but now bears the knowledge they can never be together again. In the parallel world, Rose cries and screams, begging to be taken back, but the breach is closed now, and the discs have stopped working. The Doctor places his hand on the blank wall where the breach used to be, and Rose does the same on the other side in the parallel world.
Several months later, Rose wakes up, having heard the Doctor's voice in a dream calling her. She tells Pete, Jackie and Mickey, and they get in Pete's car and follow the voice. They end up on a beach in Norway called Bad Wolf Bay, and Rose sees an image of the Doctor, who tells her they've got two minutes left and that's it, forever. She can't touch it, but they can interact. She reveals she's working with the alternate Torchwood with her experience of aliens, and that Jackie is three months pregnant. She tearfully tells the Doctor that she loves him, and he's going to reply with the same. He gets as far as "Rose Tyler..." before the image expires and he disappears. Rose sobs and runs to her family... back to her new life without the Doctor.
Back in the TARDIS, as the Doctor deals with his grief, something catches his eye: a woman in a bridal gown, facing the other way, standing inside the TARDIS. She turns, and seems just as surprised to see him as he is to see her...
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