The Doctor and Donna arrive on Earth in the TARDIS, and step outside to discover that everything is normal despite the Cloister Bell ringing in the TARDIS. The Doctor is still concerned, warning that if the walls between universes are breaking down then they’re all in deadly danger. They get into the TARDIS, unaware that the ground outside is starting to shake. Inside, the TARDIS shakes violently and when the Doctor looks out the door, there is nothing outside but the void of outer space: the Earth has vanished.
Somewhere else in the universe, Martha Jones is at the New York UNIT base and regains consciousness. Elsewhere on Earth, Captain Jack Harkness, Ianto Jones, and Gwen Cooper recover at Torchwood HQ, while Sarah Jane Smith and her son Luke put the pieces back together at Sarah Jane’s home. Wilfred and Sylvia Noble go out into the street. Everyone looks up and discovers that the sky is now filled with 26 other planets.
On an empty street, Rose Tyler appears in a flash of light, carrying an enormous rifle.
The Doctor tries to locate Earth while Donna worries about the death of her family and the other inhabitants of Earth. The Doctor is finally forced to admit defeat and sets course for the Shadow Proclamation.
The various groups on earth determine that someone has erected an atmospheric shell around the Earth to keep everyone alive. A space station hovers in space at the center of the web of planets, and 200 spaceships have launched from it and are heading toward Earth. Martha tries to contact the Doctor on her cell phone without success. Rose makes her way through the streets and chases some looters out of a television shop, then watches the news broadcasts about the approaching ships. Wilfred is unsuccessful trying to contact Donna via cell phone.
Martha contacts Captain Jack and they compare notes. Martha is involved with UNIT’s Project Indigo, a top-secret project that Jack already knows about. The airwaves are then filled with an incoming transmission from the approaching spaceships, a single word: “Exterminate!” Sarah Jane and Captain Jack recognize the voice and the threat, and prepare for the end. As Rose walks through the streets, she sees Daleks saucers overhead, firing on the buildings. Aboard their ship the Daleks prepare for the “human harvest” and launch attacks on key military centers, including the New York UNIT base.
The Doctor and Donna arrive at the interstellar headquarters of the Shadow Proclamation, an organization that acts as an intergalactic police force. The Doctor speaks with a Shadow Architect who confirms that 24 other planets have also disappeared. Thinking back, Donna remembers that a planet was mentioned as disappearing when they were in Pompeii, and that Adipose 3 had disappeared as well: both long in the distant past. The Doctor realizes that the planetary thefts have been scattered throughout time and space. Realizing that the planets can form a vast power core, the Doctor remembers that someone--or something--tried to move Earth a long time ago.
The Daleks destroy the Valiant
and Captain Jack realizes they’re going after military targets. He tries to warn Martha, but her superior General Sanchez orders her to accompany him to Project Indigo. Martha warns that it hasn’t been tested but follows orders while UNIT forces try to hold back the Daleks. Jack is in contact with her over her cell phone and warns her that Indigo will kill her. Sanchez orders her to don the Indigo unit and gives her the Osterhagen Key, authorizing her to use it as necessary no matter how dangerous it is. Sanchez and his men hold off the Daleks long enough for Martha to activate the Indigo equipment… and disappear. At Torchwood, Jack explains that Indigo is a teleport unit salvaged from the Sontaran spaceship. However, without specific coordinates, Martha has been reduced to her component atoms.
Aboard the Dalek command ship, the Supreme Dalek announces that they have conquered Earth and the Crucible is ready. However, the Supreme Dalek answers to its commander, asserting that they are beyond the Doctor’s reach. The commander doesn’t believe it and speaks of Dalek Caan, which now can see the future. The Supreme Dalek believes Caan to be an abomination but Caan speaks of the coming of the Doctor, the “three-fold man.”
As the Doctor and the Shadow Architect try to locate the missing planets, a Shadow Servant offers Donna d rink of water. However, the Servant realizes that something recently was on Donna’s back, and warns her of the loss “yet to come.” The Doctor asks Donna if she remembered anything unusual occurrence no Earth and Donna mentions disappearing bees. The Doctor realizes that some of the bees are alien immigrants, and fled Earth when they sensed minute traces of Tandocca energy. Tracking the radiation, the Doctor gets a brief signal. He prepares to leave in the TARDIS but the Shadow Architect demands that he turn over his ship to them as they prepare to go to war. She wants the Doctor to lead the effort and he agrees… then steps into the TARDIS and leaves with Donna.
Wilfred and Sylvia are running through the streets when a Dalek confront them. Wilfred tries to blind it with a paint gun but it burns off the paint and prepares to kill them. Rose arrives and destroys it, and introduces herself. She knows about Donna’s family and they go to the Noble flat. Wilfred finally tells Sylvia that Donna is traveling in time and space with the Doctor, then tells Rose he hasn’t been able to call Donna on her cell phone. Rose’s last option for finding the Doctor has failed.
The Doctor follows the Tancocca radiation to the Medusa Cascade, a vast rift in time space. The trail ends and the Doctor seemingly gives up with no idea what to do next.
The leaders of Earth have no choice but to surrender, and their new overlords order them to follow instructions and prepare for “testing.” The various groups are listening when each receives an override signal. It’s Harriet Jones, former Prime Minister, who explains via their computers that she’s using an undetectable subwave network created by the Mr. Copper Foundation. She contacts the Nobles and Rose, Sarah Jane and Luke, Torchwood, and… Martha Jones, who ended up teleporting to her family’s flat in London.
Martha informs them she has the Osterhagen Key but Harriet, knowing what it is, warns her not to use it under any circumstances. Harriet admits she still questions the Doctor’s decision to arrange for her removal from office, but knows that one day the Doctor wouldn’t be there for them. Now they must band together to summon him. Jack suggests that they use the subwave network and tie it into the world’s telephone exchanges. Using all available power, they can then boost the signal through to the Doctor’s cell phone number and let him know where they are. They proceed with the plan but Ianto warns that the Daleks will be able to detect the boosted signal and trace it to the source: Harriet Jones. Realizing that she’s doomed, Harriet says she’s willing to make the sacrifice and they go ahead with the plan.
The Doctor’s cell phone rings inside the TARDIS and the Doctor works to track the signal. The Daleks also sense the leader and their commander warns that his minions were too overconfident. The Daleks land at Harriet’s flat and she transfer the subwave network to Jack and Ianto at Torchwood. She defiantly faces the Daleks as they enter and they ruthlessly gun her down. Aboard the TARDIS, the Doctor follows the signal and realizes that Earth and the other 26 planets have been pulled into a time rift one second out of sync with the rest of the universe. He contacts the various groups, although is unable to see Rose since the Noble computer doesn’t have a webcam. However, the Daleks’ leader taps into the subwave network as well. The Doctor and Sarah Jane both recognize his voice: it’s Davros, creator of the Daleks. Davros supposedly died during the Time Wars, but Dalek Caan made an emergency temporal shift and managed to breech the timelock barriers placed around the wars. Caan was driven insane but gained the gift of prophecy. Now Davros has made a new race of Daleks from his own cells and plans to conquer the universe. The Doctor materializes the TARDIS on Earth but Davros is aware of where he’s heading. Dalek Caan, seeing the future once more, notes that the Doctor will suffer the death of his “most faithful companion.”
The Daleks locate the subwave network at Torchwood and prepare to attack. Jack gets her teleport base code and uses it to program his own device, then teleports out to find the Doctor while leaving Ianto and Gwen to hold the fort.
Sarah Jane orders Mr. Smith, her super-computer, to protect Luke while she goes to find the Doctor.
Rose locates the TARDIS with her equipment and goes to find it.
The TARDIS materializes it and the Doctor wonder where the Daleks have taken all the people. Rose finds them and the two run to greet each other… and a Dalek guns down the Doctor. Captain Jack appears just a second too late, and destroys the Dalek.
Ianto and Gwen prepare to defend themselves, although they’re aware their guns won’t work against Dalekenium casings.
Jack, Rose, and Donna get the dying Doctor into the TARDIS. The Doctor’s hand begins to glow with Artron energy.
Sarah is driving down the streets when two Daleks block her way. They prepare to kill her.
The Daleks enter the Torchwood facility and prepare to kill Ianto and Gwen.
As Donna explains the regenerative ability of Time Lords to Donna, the Doctor staggers to his feet and glows with energy…