Rose is on a beach, saying that she is telling the story of Torchwood, the last story she'll ever tell... and the story of how she died.
Rose identifies the Daleks as they approach her, and informs them that she knows all about them and the Time War. She demands that they keep her alive so she can tell them what they know, and Mickey and Singh play along. The Daleks agree and check on the status of something they've brought with them from the void ship, the Genesis Ark. They plan to protect it at all costs.
In the control center, Jackie asks what has happened to Rose, and the Doctor admits he doesn’t know. He promises to get both of them out. Meanwhile, the Cyber Leader tells Yvonne to patch it into the global authorities so it can address the world. It goes on the air and informs humanity that the Cybermen have now taken over the planet and will convert everyone into Cybermen, removing fear, sex, and class. Across the world, the military try to fight back without success as the Cybermen relentlessly advance. From Torchwood Tower, the Cyber Leader asks why humanity isn't surrendering, and the Doctor notes that humanity will fight back.
The Daleks demand to know which of the three are the least important. Rose refuse to answer, but Singh admits that it's his responsibility and volunteers himself. The Dalek demands that he kneel and he reluctantly obliges, and they then surround him and attach their plungers as he screams in agony.
The Cybermen detect the Dalek activity and send units to investigate.
Singh is reduced to a desiccated husk and the Daleks realize that the Cybermen have invaded posing as ghosts. Dalek Thay goes to investigate and encounters the two scouting Cybermen. They open a visual link to the Cyber Leader, while the Daleks monitor Thay's visual input. Both sides refuse to yield. Meanwhile, the Doctor calls Rose on her cellphone and confirms that she's alive. He wonders why they need her, and overhears them mention the Genesis Ark. The Cybermen suggest an alliance, but Thay dismisses them as inferior. They open fire but the Dalek is proof against their weapons and easily destroys them. The Cyber Leader opens the link and warns them that they are preparing a war, but the Daleks are confident they can handle the millions of Cybermen. However, the Daleks spot the Doctor in the background of the broadcast. They identify him as their enemy and notice that Rose's heartbeat increased when she saw him. She identifies him and realizes that they're frightened.
The Cyber Leader orders its units to take away Jackie and the others for conversion into new units, and ignore the Doctor's protests.
The Daleks prepare to open the Genesis Ark, while Mickey wonders why they want Rose.
Yvonne and Jackie are taken to the construction area and they realize what is in store for them. The Cybermen take Yvonne in as she insists she did her duty for Queen and country. She shrugs off her captors and marches in, proud. Jackie watches in horror as Yvonne is "upgraded."
The Cyber Leader tells the Doctor that he is proof that emotions are destructive. The Doctor looks up in hope as Jake and his men teleport in from the parallel world and destroy the Cybermen.
Jackie is taken for conversion but the Cybermen halt when they realize that the Cyber Leader has been destroyed. One of her captors is upgraded to Cyber Leader, and Jackie takes advantage of the distraction to run away.
Jake orders his men to secure the area, while Jake gives the Doctor the dimension-jumping technology that their version of Torchwood has developed. He teleports the Doctor to the other Earth, and explains that the People's Government took control of the Torchwood Institute. Pete comes in and informs the Doctor that he's in charge, and the Doctor will listen for once.
Mickey explains that he can teleport out using his device, but it will only take one and he won't abandon her. When he wonders why the Daleks want him, Rose remembers how she reactivated a Dalek by touching it, and that she absorbed background radiation from time travel. The Daleks evolved to use it as a power supply, and they both have traveled in the TARDIS. Mickey wonders why the Daleks built something they can't open, and the Daleks explain that the Time Lords built the Genesis Ark.
Pete explains that they sealed the Cybermen inside of the factories, but people argued against their destruction on the grounds they were humans. Meanwhile, the Cybermen infiltrated Torchwood, adapted the technology, and crossed the void to the Doctor's world. When the Doctor points out that Rose is his daughter, Pete insists that she is the daughter of a dead man. Their world is at peace under Harriet Jones, but the world's temperatures are rising. The Doctor explains that the breach is causing the environmental disruption, and both worlds will soon be destroyed. The Doctor admits he can seal the breach, but it will leave the Daleks on the Doctor's world. Pete is unimpressed, but the Doctor reminds him that there is still a Jackie alive. Pete asks him for help and the Doctor agrees.
The Doctor, Pete, and Jake teleport back to the Doctor's world and the Doctor calls Jackie. She eventually tells him where she is, and the Doctor cuts her off. He then grabs Jake's gun and confirms it can destroy a Cyberman. The Doctor then surrenders to the Cybermen.
The Daleks inform Rose that she should open the casket, and she reluctantly agrees when they threat to kill Mickey. However, first she offers to tell them that the Emperor Dalek survived... until she destroyed it. They prepare to destroy her, but the Doctor comes in. They detect no weapons and insist he's powerless, and ask how he survived the Time War. The Doctor says he fought on the front lines, and points out that they fled. The Daleks explain that they have names, and the Doctor realizes they are part of the Cult of Skaro, Daleks programmed to imagine. He doesn't recognize the Genesis Ark, and the Daleks insist they will use Time Lord technology to reestablish their supremacy. The Doctor realizes they have to touch to open it, and refuses to help them. He then shows them the sonic screwdriver and opens the door. The Cybermen and Jake's soldiers, working together, break in and open fire. Pete gets Rose out while Mickey opens fire. However, a stray shot knocks him back and he inadvertently touches the Genesis Ark. Mickey gets out with the others while the Daleks destroy the Cybermen and move the Ark outside.
Jackie escapes down the stairs but finds Cybermen coming up toward her. She retreats but more Cybermen cut her off. However, Pete destroys them as he arrives with the others. He's shocked to see her and vice versa. Jackie finally admits that she never found anyone else, but Pete admits he's glad to see that she raised Rose as the daughter he never had. However, he insists that she's not his wife, but then finally gives in and runs to her. Jackie runs to him and they embrace.
The Daleks move the Genesis Ark out through the Torchwood complex, destroying everything in their path. The Cybermen weapons are useless against them. Torchwood soldiers open fire as well but are equally useless. The Cyber Leader calls in all of its units to Torchwood to aid in the effort.
The Doctor runs in and grabs the magna-clamps that Yvonne showed him earlier, and then retreats to the others. The Daleks open the roof hatch and fly up into the sky, while the Doctor tries to determine what Time Lord science is within the Genesis Ark. He and the others run for the control center. They watch as the Genesis Ark opens and millions of Daleks emerge: the Ark is a prison ship, and bigger on the inside than the outside. The Daleks fly out across the city, opening fire on the approaching Cybermen and fleeing humans alike.
Pete realizes that it's a lost cause and prepares to leave, taking Jackie with him. The Doctor says he's ready to close the breach and explains that he has glasses that can detect void radiation. He plans to open the void, sucking everything that passed through it back into the gaping energy. However, Rose realizes that she has the same energy and will be pulled in. The Doctor admits she's right, and that she'll have to go back with the others. The void will close itself, and the Doctor will use the magna-clamps to avoid being pulled in. Rose refuses to abandon her world, and Jackie refuses to abandon her daughter. Rose says that her mother has to go, but she can't leave the Doctor. However, the Doctor places a teleport amulet on her and Pete teleports herself and the others to the world. Rose quickly activates it and returns. Pete stops Jackie from going back, saying that they can't further open the breach.
Rose returns and tells the Doctor she won't leave him, and that she promised to always stay with him. Giving in, the Doctor tells her to operate the controls.
The Cybermen head for the control center to return to their own world. However, a Cyberman opens fire on them and insists that it is doing its duty for Queen and country. As it kills them, a single oily tear falls from its eye.
The Doctor and Rose activate the device and fasten the magna-clamps to the walls. The Daleks detect their activity and move in for the kill, and the doctor and Rose activate the particle accelerators. The void opens and the Daleks are pulled in. On the ground below and across the world, the Cybermen are pulled up and into the void. Outside, the Cult of Skaro initiate a temporal shift, disappearing with the Genesis Ark.
The Doctor and Rose watch as the Daleks are pulled past them. However, the particle accelerator next to Rose shorts out and the lever starts to open. She lets go of the magna-clamp and pulls the lever back online. The remaining Daleks are pulled through, but Rose starts to lose her grip on the lever as the Doctor looks on helplessly. She's finally pulled loose, but Pete teleports in, grabs her, and teleports back to his world.
In the other world, Rose pounds on the wall in helpless fury. Pete looks at the teleport device and confirms that it's no longer working now that the Doctor has closed the breach.
The Doctor looks at the void wall for a long moment, and then turns and walks away.
Some time later, Rose is sleeping and has a dream of the Doctor calling to her. She tells Pete, Jackie, and Mickey, and they pack up and follow the voice to a deserted stretch of beach in Norway, a beach named "Bad Wolf.". A hologram of the Doctor appears. He explains that there's a tiny bit of the breach open, and he's using the energy of a supernova to communicate. The Doctor warns they only have two minutes, and Rose tells him that Jackie is pregnant. He wonders about her, and Rose explains that she's working with that world's Torchwood. The Doctor then admits he admires her for living the life he can never have, a life that progresses normally, day by day. Rose wonders if she'll ever see him again, and the Doctor says she can't and that he'll jus move on with his life, doing what he's always done. Rose, in tears, says that she loves him. The Doctor tries to respond in kind, but the power cuts out and the hologram disappears.
The Doctor finds himself back in the TARDIS, shedding a single tear.
Jackie runs to her crying daughter and embraces her.
After a moment, the Doctor goes to the TARDIS consoles and prepares to depart. However, an angry woman in a white dress appears and demands to know where she is, much to the Doctor's shock and surprise.