The TARDIS arrives on Earth and the Doctor and Donna emerge, but everything seems fine. However, the Doctor warns that if Rose could come to "their" universe from her parallel world, then the walls of the universe are breaking down. As they return to the TARDIS, a milkman's bottles start to vibrate and the entire world begins to vibrate.
Inside the TARDIS, Donna wonders if the Doctor's return is good. He hesitatingly admits it is. Suddenly the TARDIS shakes and the Doctor runs to the doors and opens them to reveal… the void of space. The TARDIS is in the same place, but Earth has disappeared.
Far across the universe…
In New York, Martha Jones recovers consciousness in the wreckage of UNIT. Captain Jack Harkness is with Torchwood, while Sarah Jane and Luke try to determine what is going on. Wilfred and Sylvia are equally confused. They all look to the sky... to see they are in another galaxy with 26 other planets nearby. And in the street where the TARDIS appeared, Rose Tyler appears with a large energy gun.
The Doctor and Donna try to determine Earth's location, and Donna worries that everyone is dead, including her family. The Doctor can't find a trace and takes Donna to the Shadow Proclamation.
On Earth, Jack, Gwen Cooper, and Ianto Jones are trying to find out what the problem is and determine that someone has established an artificial atmospheric shell, keeping Earth's inhabitants alive. They also spot something else: a space station at the center of the web. Sarah Jane and Smith have used Mr. Smith, the super-computer, to confirm the same thing. Two hundred spaceships move in, and UNIT prepares for battle. Martha is unable to get hold of the Doctor on her cell phone. Rose makes her way through the streets, where people are rioting at the apparent end of the world. When she spots two looters at a television shop, she tells them to run and then watches the news broadcasts. Sylvia and Wilfred are watching the same broadcast, and Wilfred is unable to contact Donna on his cell phone.
Martha calls Captain Jack who confirms he hasn't heard from the Doctor either. Martha mentions Project Indigo, a top-secret program that Captain Jack already knows about. They all receive an incoming transmission from the spaceships: "Exterminate!" Captain Jack and Sarah Jane all realize the end is near, but Rose strides out into the ships and looks overhead to see the ships arriving and opening fire. She strides away as buildings burst into flames. The Daleks prepare for the "human harvest" while UNIT swings into action… as the Daleks open fire on their New York headquarters.
The Doctor and Donna arrive at the Shadow Proclamation headquarters, as the Doctor explains they're an intergalactic police force. The Doctor and Donna emerge to confront the Jadoon patrolmen. After identifying himself, the Doctor meets with a Shadow Architect, who says that Earth has disappeared along with 24 other planets. Donna recalls a planet mentioned during their visit to Pompeii as well as Adipose 3. Although the Shadow Proclamation is unimpressed, the Doctor realizes planets have been stolen from time as well as space. The planetary display automatically aligns the planets in balance and the Doctor realizes they represent some kind of engine. He remembers someone else tried to move the Earth long ago…
The Daleks destroy the Valiant air carrier and Captain Jack warns Martha that the Daleks are targeting military bases. General Sanchez orders Martha to accompany him: Project Indigo is to be activated. Martha warns it hasn't been tested but they head to the labs while the UNIT soldiers try to hold the Daleks back. Sanchez orders Martha to don the Indigo power pack and gives her the Osterhagen Key, authorizing her to use it as necessary. The Daleks close in and Sanchez fights a last-ditch effort as Martha activates the Indigo unit: a teleportation unit. Jack explains that it's an experimental teleport salvaged from the Sontarans, but without coordinates Martha was scattered into atoms.
The Supreme Dalek announces that the Crucible has been prepared, while a shadowy figure asks if the Doctor has been spotted. The Supreme Dalek assures its superior that they are beyond the Doctor's reach. Its superior speaks of Dalek Caan, which the Supreme Dalek views as an abomination. Caan says that the "three-fold man," the Doctor, is coming.
Donna waits while the Doctor tries to figure out the location of the planets. A Shadow Servant offers Donna water and realizes there was something on her back. She then expresses sorrow about Donna's loss: the loss "yet to come." The Doctor asks if she remembers any unusual weather patterns, and Donna mentions bees disappearing. The doctor releases at least some of the bees are aliens, and went back home when they realized danger was coming. The alien bees are sensitive to Tandocca energy, and he tracks the radiation. The Shadow Architect declares war on the thieves and asks the Doctor to lead them into battle, co-opting his TARDIS. He steps inside to get the key… and dematerializes the TARDIS.
Wilfred and Sylvia are fleeing through the street when they run into a Dalek. Wilfred tries to blind it without success and it prepares to kill them. However, Rose arrives and guns I down, then recognizes them as Donna's family. Wilfred tries to explain to Sylvia where Donna has been all this time, while Rose admits that if they can't find Donna then they can't find the Doctor.
The TARDIS arrives at the Medusa Cascade, a vast rift in time and space. However, the trail is dead and the Doctor has no idea what to do.
Earth surrenders to the Daleks and the Daleks order humans to prepare to follow instructions for testing. However, the Nobles, Rose, Sarah Jane, and Torchwood have their signals intercepted and former prime minister Harriet Jones establishes contact with all of them, including Martha who has teleported to her home in England. She explains the subwave contacted is safe from interception and was developed by the Mr. Copper Foundation. Martha says she has the Osterhagen Key and Harriet says it is not to be used under any circumstances. Harriet needs the Doctor but knew that the Doctor wouldn't appear at the time when they needed him most. They have to form a secret army and Jack suggests they boost the subwave generator through every telephone exchange using the power of the rift, and the amplified signal will reach the Doctor. However, Ianto warns that if they all transmit then the Daleks will trace the signal back to Harriet, but she believes the sacrifice is worth it. They all go to work and make the call.
Aboard the TARDIS, the Doctor's phone ring and the Doctor follows it. Meanwhile, the Doctor's detect the signal and track it to the point of origin. The Daleks' shadowy leader warns that the Daleks were overconfident, but everything is moving into place. A Dalek saucer moves in on Harriet's location and she transfers the subwave network to Torchwood while saying it's an honor. She turns to face the invading Daleks and they gun her down as she defies them.
The TARDIS is pulled one second into the future and to Earth and the other 26 planets. The entire Medusa Cascade has been put one second out of sync. The Doctor taps into the subwave network and they are all reunited.
The Daleks' commander taps into the subwave network and talks directly to the Doctor. Sarah Jane recognizes the voice as does the Doctor: Davros, lord and creator of the Dalek race. The Doctor had thought Davros destroyed in the Time War, but Dalek Caan had made an emergency temporal shift and bypassed the timelock placed on the struggle. Caan was driven insane but Davros escaped and made a new race of Daleks, grown from cells of his own body. The Doctor says only one thing--"Bye"--and leaves. Davros assumes he's heading for Earth, while Caan sees a future with the death of the most faithful companion.
The Daleks locate Torchwood and move in. Jack contacts Martha and has her give him the teleport base code. He uses his own teleport device and goes to find the Doctor, promising Gwen and Ianto he'll be back. After he disappears, the Daleks move in to the facility.
Sarah Jane goes to find the Doctor, using Mr. Smith to find the coordinates. She tells Luke to stay, ordering Mr. Smith to protect him.
Rose locks onto the TARDIS and Sylvia and Wilfred wish her luck.
The TARDIS materializes in London and the Doctor and Donna discover the Daleks were taking the people. Rose finds them and she's reunited with the Doctor as Donna looks on, smiling. They're unaware that a Dalek is watching them… and shoots the Doctor. Captain Jack appears and destroys it a second later.
Gwen and Ianto prepare to make a fight of it.
Rose, Jack, and Donna get the Doctor into the TARDIS. Jack orders them to step back, warning Rose that she knows what happens next. The Doctor's hand begins to glow as he regenerates.
Sarah runs into a Dalek road block. She surrenders but they prepare to exterminate her regardless.
The Daleks penetrate the Torchwood facility and Gwen and Ianto open fire.
The Doctor staggers to his feet while Rose explains to Donna about regeneration. The Doctor glows with energy…