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 removed from existence, but thanks to their creation, the Pandorica, the Doctor reversed the damage done by the Silence and restored them to their proper times without memory of their alliance.