River Song is serving a sentence for a crime she can’t remember committing. She has been imprisoned in the Stormcage Containment Facility for murdering the Doctor in The Wedding of River Song. River Song was actually an assassin engineered by the Silence to kill the Doctor. She was forced into an astronaut suit and made to wait beneath Lake Silencio in Utah, USA. When the moment came, she shot the Eleventh Doctor in front of Amy Pond, Rory Williams and her younger self (The Impossible Astronaut/Day of the Moon). River Song was later working towards being pardoned for her crime under the custody of Father Octavian (The Time of Angels/Flesh and Stone). River Song had been pardoned for her crime by the time of the events of The Angels Take Manhattan.