The Pandorica Alliance, (PROSE: The Monster Vault) also known to historians as the Alliance of Enemies (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) and referred to by its own membership as simply the Alliance, was an association of diverse races, mainly 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 his TARDIS would cause the cracks in time, which in turn would end all of existence. In truth, the blame belonged to Madame Kovarian and her faction of the Silence in one of their many blunders in an attempted murder of the Doctor.
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In the "Total Collapse Event Incident", the Alliance devised a plan to trap the Doctor in a specially-built prison known as the Pandorica to prevent him from piloting his TARDIS. However, none of them knew River Song could pilot the TARDIS as well, which led to the explosion. They were temporarily erased from existence, but thanks to their creation, the Pandorica, the Doctor negated the destruction caused by the Silence and restored them to their proper times without memory of their alliance.
History
A day to come
The Time War-era Time Lords became aware of the Alliance through the Matrix's projections of the post-Time War universe, deeming it the most noteworthy Dalek alliance beyond even the earlier Intergalactic Council. (PROSE: Dalek Combat Training Manual)
Following the Time War, the Nestene Consciousness first conceived of an alliance with the Doctor's greatest enemies after surviving a defeat by the Ninth Doctor's hand. Seeking vengeance, it decided to destroy the Doctor by forming this alliance, in order to "rid the universe of this pestilance". The Dalek and Cyberman empires were prime candidates for this brewing plan. (PROSE: Revenge of the Nestene)
The Alliance
The Alliance was finally brought to fruition in response to the cracks in time caused by the explosion of the Doctor's TARDIS, with many of its members joining in order to "save the universe from [the Doctor]".
Members of the Alliance visited 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 Nestene creating Autons disguised as a small legion of Roman soldiers from a picture book that Amy owned. They were set near Stonehenge, also featured in the picture book, in the year 102 AD. Among the Auton duplicates was a copy of Rory Williams. The Pandorica, named for "Pandora's Box", another book Amy owned, was placed under Stonehenge. A Cyberman was placed with the Pandorica to act as a sentry, but was heavily damaged before ultimately being destroyed by the Auton duplicate of Rory. (TV: The Pandorica Opens)
As the Total Collapse Event Incident began to trap the Doctor, (PROSE: Dalek Combat Training Manual) Stonehenge acted as a transmitter, summoning members of the Alliance to converge on the Pandorica when the Doctor arrived. The Doctor managed to keep them at bay for an hour by extending the Pandorica's force-field technology around Stonehenge; he also warned them to "do the smart thing" by letting someone else try first due to how many times he's defeated them in the past. Once the Pandorica was ready to open and hold the Doctor indefinitely, a high-pitch signal went out to the Auton copies and activated their programming; however, Rory's copy possessed the heart and soul of the original, allowing him to fight back. (TV: The Pandorica Opens)
Led down to the surface by the Supreme Dalek, (PROSE: Dalek Combat Training Manual) the Alliance confronted the Doctor and explained their intentions. They had concluded that the cracks would be caused by the destruction of his TARDIS; therefore they sealed the Doctor inside the Pandorica to prevent him from using it, believing only he could pilot the TARDIS and this would avert the disaster. As they sealed him inside, the Doctor tried to save them and the entire universe, warning them desperately that he was not the one responsible. However, unknown to them, River Song, the Doctor's wife and companion, could also pilot the TARDIS. She was attempting to do so at that time, which caused the destruction of the universe. (TV: The Pandorica Opens)
Legacy
The Alliance's plan failed and all the Alliance species, including the Daleks, Cybermen, Judoon, Sontarans, indeed, everything in the entire Universe save the Earth and Moon, were erased from existence, leaving only stone 'after-images' behind. The stars, including the Sun, no longer existed, because they all went supernova at the same moment. According to the Cybermen, all alternate universes and the Void were also erased from existence. Ironically, the Alliance's attempt to save the universe destroyed it.
The Doctor piloted the Pandorica into the TARDIS explosion, creating a second Big Bang that "rebooted" the universe. This erased the cracks from existence.
As the Pandorica was used to save the universe, the Alliance helped the Doctor in the effort, so their plan did succeed. However, as the cracks never existed, the Alliance never had a reason to form in the new version of the universe and the members of the Alliance were restored to their original forms and places in space and time. (TV: The Big Bang) However, human historians knew of the Alliance, (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe) and the 1995 book A Directory of Impossibilties by Wilson Ryder and Harriet MacMillan later recalled the legend of the Lone Centurion which guarded the Pandorica, which was republished in The Secret Lives of Monsters. (PROSE: The Secret Lives of Monsters)
Human historians following the Siege of Trenzalore acknowledged the "Alliance of Enemies" within a string of defeats, following the Eye of Time and the Eternity Clock and preceding the Dalek Project and the Dalek Foundation, the Doctor inflicted on the New Paradigm which led to their organisational restructure into the Parliament of the Daleks preceding the Asylum Incident. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)
Known individuals
Known individuals in the Alliance included a Cyber-Leader, a Supreme Dalek, an Eternal Dalek, a Drone Dalek, a Roman Commander, Claudio, Marcellus, an Auton Rory Williams, Commander Stark, a Judoon Captain, three Silurians, a Hoix, two Roboforms, a Sycorax, a Uvodni and a Blowfish. (TV: The Pandorica Opens)
Other references
Mr Smith was aware of the formation of an Alliance of Enemies of the Doctor. (TV: SJAF 4)