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Template:Infobox Organization The Alliance was a large group of aliens, including many of the Doctor's enemies, formed to stop the greatest threat in the universe, which they all believed to be the Doctor. They predicted that the explosion of the TARDIS would cause the cracks in time, which in turn would end all of existence. They devised a plan to trap the Doctor in a specially built prison known as the Pandorica.
History
Members of the alliance travelled to Amy Pond's house, the night she left with the Doctor,. By tracing the psychic imprints there, they were able to sample Amy's memories and use them to create a scenario the Doctor would not be able to resist, as a way to lure him to the Pandorica. This resulted in the creation of a small legion of Autons. disguised as Roman soldiers from a picture book that Amy owned during her childhood. They were placed near Stonehenge, also featured in the picture book, in the year 102 AD. Among the Auton duplicates was a copy of Rory Williams, presumably created because a photograph of Rory in a Roman centurion costume was kept within the pages of the book. The Pandorica, named for "Pandora's Box", another book Amy enjoyed as a child, was placed under Stonehenge.
Stonehenge acted as a transmitter, allowing the alliance members to converge on the Pandorica when the Doctor arrived. Representatives of the alliance confronted the Doctor and explained their intentions. As they had concluded that the cracks would be caused by the destruction of his TARDIS, they sealed the Doctor inside the Pandorica to prevent him from using it, believing that only the Doctor could pilot the TARDIS. This should avert the disaster.
However, unknown to them, River Song, one of the Doctor's companions, could also pilot the TARDIS, and was attempting to do so at that time, an action which caused the destruction of the universe.The Alliance's plan thus failed, and as a result, several species, including the Daleks, Cybermen, Judoon, Sontarans and all other members of the Alliance were wiped from existence, leaving only stone "after-images" behind. (DW: The Pandorica Opens)
One Dalek was later revitalized by the restoring energies of the Pandorica, and attacked the released Doctor and his allies. River Song destroyed it by shooting it in its eyestalk while its power was depleted.
The Doctor threw the Pandorica into the TARDIS explosion, creating a second Big Bang that "reset" the universe, removing the cracks themselves from existence. Technically, due to the Pandorica being used to save the universe, the Alliance helped the Doctorin the effort and thus their plan did succeed. As the cracks never existed, the Alliance itself was never formed. All members of the Alliance were restored to their original forms and places in space and time. (DW: The Big Bang)
Despite the erasure of the Alliance, it somehow returned. The Alliance locked the Doctor in a second Pandorica, though this plan was soon foiled with the assistance of the Shoppers. (DW: The Doctor Who Experience)