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The Alliance was a large group of many different races, including many of the Doctor's enemies, formed to stop the greatest threat in the universe, which they all believed to be the Doctor; it was actually the Silence. They predicted that the explosion of his 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.
- For other uses of the term "Alliance", see Alliance.
History
Members of the Alliance travelled to Amy Pond's house the night she left with the Eleventh Doctor in 2010. They traced the psychic imprints there, sampled Amy's memories and used them to create a scenario the Doctor could not resist 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 in 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 in 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 members of the Alliance 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 only he could pilot the TARDIS and that this would avert the disaster. As they sealed him inside, the Doctor tried to save them and the entire universe, attempting desperately to warn them of the true threat.
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, which caused the destruction of the universe. The Alliance's plan failed, and all the Alliance species, including the Daleks, Cybermen, Judoon, Sontarans and indeed everything in the entire Universe, save the Earth and Moon, were wiped from existence, leaving only stone 'after-images' behind. The stars no longer existed, due them all simultaneously going supernova. (DW: The Pandorica Opens)
The Doctor piloted the Pandorica into the TARDIS explosion, creating a second Big Bang that "reset" the universe. This removed the cracks from existence. Technically, due to the Pandorica being used to save the universe, the Alliance helped the Doctor in the effort, so their plan did succeed. As the cracks never existed, the Alliance itself was never formed. The members of the Alliance were restored to their original forms and places in space and time. (DW: The Big Bang)