The Alliance is a large and possibly uncountable amount of aliens all joined up to stop the greatest threat in the Universe, which they all believed to be the Doctor. They predicted and calcualted that a explosion of the TARDIS would cause the cracks in time that were dangerous to all of the members, along side the rest of the universe, and other universes/voids. They came up with a plan to trap the Doctor and to bring him to The Pandorica, where they would then imprisoned him inside it. As they knew that the Cracks would be caused by the explosion of the TARDIS, they sealed the Doctor inside to prevent him from doing so, however, they did not know that River Song one of the Doctors, future, companions could fly the TARDIS aswell.