When the Earth is stolen from its orbit and placed in another galaxy with 26 other stolen planets, the Doctor's secret army of allies comes together to defend the Earth from the new Dalek Empire. With battles raging on the streets and in the sky, the Doctor and Donna confront the Shadow Proclamation to find the truth; however, a fearsome old enemy waits in the shadows.
The Tenth Doctor and Donna Noble arive on Earth immediately following the events of Turn Left. They rush out of the TARDIS to find the Earth as normal. They ask a nearby milkman the day and ascertain nothing is wrong.
They re-enter the TARDIS to try and work out what caused the Bad Wolf warnings to appear. Whilst inside the TARDIS shakes violently and the Doctor rushed to the door and opens it to find the TARDIS is now floating in outer space, the TARDIS has not moved however, the Earth has been stolen from underneath them.
Meanwhile on Earth, the Doctor's companions, Sarah-Jane Smith, Torchwood, and Martha Jones all look to the sky outside and see 26 planets, as well as earth all orbiting a common centre of mass inside a nebula in space.
Meanwhile the Doctor and Donna travel to the Shadow Proclamation, manned by Judoon and humanoid females with white hair and red eyes. Whilst there the Doctor discovers that 24 planets have disappeared immediately before their arrival. Donna remembers a number of other planets and moons which they were told had disappeared in earlier adventures, including Pyrovillia and Adipose 3.
One of the humanoid females provides Donna with refreshment and cryptically tells her she is sorry for her future loss. Donna and the Doctor ascertain that in the time before the Earth being stolen, bees were disappearing from the planet which emitted carrier waves to where the planet would be taken to. The Doctor then runs to leave in the TARDIS whilst one of the Humanoids orders the Doctor to surrender the TARDIS to them so that he could lead them to war. The Doctor escapes before the Shadow Proclamation can commandeer the TARDIS.
On Earth, Rose Tyler appears in a high street where widespread chaos and looting is in progress. She enters a computer store and hacks into UNIT computer systems. UNIT detects 3000 space ships approaching the Earth and the UN in Geneva declares an "Ultimate Code Red" as the ships transmit a message to Earth composed of only the word "Exterminate!".
Captain Jack Harkness in Torchwood 3 calls Martha Jones in New York with UNIT, whilst her commanding officer orders her to initiate the "Project Indigo". Martha is surprised to learn that Jack knows of the existence of "Project Indigo", Jack explains to Ianto that it is teleportation device based on recovered Sontaran technology, which UNIT are still trying to perfect. Martha and her commanding officer leave the main office just in time to avoid extermination by the Daleks which have arrived on Earth and have begun attacking military installations, including the Valiant which is destroyed by swarming Daleks. Martha escapes to a back room and is ordered to put on a harness which is apparently a prototype device resulting from the "Indigo Project". She is given a device called the Orstenhagen key by her commanding officer and ordered to activate the teleportation harness. She does so and disappears immediately before her commanding officer and his aide are exterminated by Daleks.
Donna Noble's mother and grandfather are hiding in a back alley, armed with a paintball gun, as they watch the Daleks order everyone in the street from their homes. One family refuses to comply and retreats backs in to their home. Three Daleks converge and destroy the house, presumably with the family inside. Donna's family retreat to their own home but are stopped by a Dalek on the way. Donna's grandfather shoots the Dalek's eyestalk with the paintball gun, but the Dalek vapourises the paint declaring "My vision is not impaired!" and prepares to exterminate him. However immediately before it can, Rose Tyler destroys the Dalek with her weapon.
They retreat to the Noble's house as a laptop comes to life with former Prime Minister Harriet Jones communicating with all the Doctor's Companions on Earth by an unnoticeable sub-wave communications network. Torchwood, Sarah-Jane (via Mr Smith) and Martha Jones all communicate via a conference video call. Rose Tyler can only watch however as the Noble's never bought a webcam for their PC.
They establish that everyone with superphones have been unable to contact the Doctor. They together come up with a plan to boost the signal using the power of the rift and the coordination of Mr Smith to break through whatever the interference with the signal is. However the increased power of the resulting signal will make the communication network noticeable and traceable to the Daleks.
Meanwhile the Doctor in the TARDIS has followed the trail to its end and they arrive at the Medusa Cascade, apparently with no way to follow the signal further, the Doctor concludes that there is no way to find where all the planets have gone. The signal from Torchwood breaches the barrier however and begins to ring the Doctor's superphone. He uses the signal to trace where the Earth has been taken to and sends the TARDIS back to the source. He concludes that the Cascade has been placed 1 second out of phase with the rest of the universe and the 27 missing planets appear in front of them.
Meanwhile a shadowy figure inside the Daleks central command orders the Supreme Dalek to patch him to the sub-wave network after sending Daleks to the source of the network at Harriet Jones's house, where it appears she is exterminated off screen. Davros appears on the screen in the TARDIS and declares to the Doctor that Dalek Caan arrived on his ship in the time war after his emergency temporal shift despite the Time War being time locked, succeeding where the Doctor had failed and rescued him from the War. Davros also reveals he has rebirthed the Dalek race by cannabilizing his own body, he opens his shirt to reveal his remains of his exposed organs and skeleton.
The Doctor abruptly cuts the transmission and dematerialises the TARDIS and lands on Earth. Captain Jack gains some information from Martha Jones about the Indigo project which he uses to reactivate his wrist device. He then teleports to the location of the TARDIS but not before telling his Torchwood colleagues that he'll be back for them. He leaves and a Dalek breaks through into the hub as Ianto Jones and Gwen Cooper fire machine guns to defend themselves. At the same time, presumably on her way to find the Doctor, Sarah Jane Smith leaves Luke Smith under the care of Mr Smith and takes off in her car, only to be stopped by Daleks who reject the concept of apologies or surrender, and prepare to EXTERMINATE her.
Rose communicates to Torchwood in her own universe and tells them to transmat here to the Doctor's location. Rose arrives as the Doctor and Donna steps out of the TARDIS and the two see each other. As they run towards each other a stray Dalek emerges from behind a van and shoots towards the Doctor. It is only a glancing blow but some of the beam hits his arm and sends the Doctor to the ground. Captain Jack materialises and destroys the Dalek with his gun. Together they drag the Doctor into the TARDIS and the Doctor proclaims he is beginning to regenerate, and light begins shooting out of his body as his regeneration occurs.