Kovarian Madame Kovarian was an associate of the religious movement the Silence , representing the Kovarian Chapter . History . Frustrated by the centuries - long conflict involving the Eleventh Doctor , the Papal Mainframe and the various enemies of the Doctor during the Siege of Trenzalore , Kovarian and her followers travelled back through time to prevent the siege from occurring . Her first attempt involved blowing up The TARDIS , ( TV : " The Time of the Doctor " ) though this only created the cracks in time and destroyed the universe , forcing the Doctor to repair the damage she caused . ( TV : " The Big Bang " ) Her second attempt involved " [ engineering ] a psychopath to kill " the Doctor . ( TV : " The Time of the Doctor " ) Creating River Song . Some time after Amy ' s honeymoon , Kovarian arranged her abduction and replacement by a Ganger . Amy ' s real , pregnant body was taken to Demons Run in the 52nd century . Kovarian watched over her through a hatch above the room Amy was held in . Meanwhile , her linked Ganger lived out her life . This affected the Ganger ' s mind . She saw visions of Kovarian wherever she went , often hearing her comments on her health and her pregnancy . ( TV : " A Good Man Goes to War " ) Monitoring Amy . The first time Ganger Amy saw Kovarian , she appeared at the little girl ' s bedroom door at Graystark Hall Orphanage in a hatch in the door . Amy was startled and asked who she was . Kovarian ignored her and said " No , I think she ' s just dreaming " , then disappeared . The room was empty , with no evidence of Kovarian or the hatch . ( TV : " Day of the Moon " ) While sleeping on a pirate ship , Amy woke to see Kovarian in a hatch that opened on the hull . She said , " It ' s fine . You ' re doing fine . Just stay calm . " When Amy looked away , she vanished along with the hatch . ( TV : " The Curse of the Black Spot " ) She was seen twice by Ganger Amy at an acid mining factory , first whilst Amy searched for Rory , though she did not speak . The next time , Amy sensed her coming appearance and stared at the wall where the hatch would open . ( TV : " The Rebel Flesh " ) After her Ganger form was destroyed , Amy awoke to find herself in an alien hospital and heavily pregnant , with Kovarian looking over her . She went into labour , with Kovarian cruelly instructing her to push . ( TV : " The Almost People " ) The Battle of Demons Run . Madame Kovarian and Colonel Manton visited Dorium Maldovar to ask him what he knows ; they had been on Yellow Alert for a month and the Doctor hadn ' t done anything . Dorium explained that there were numerous people throughout time and space who owe the Doctor a debt for helping them ; he ' s gathering an army . Dorium explained the stories about the Doctor were true and not myths . Seeing they were getting nowhere , Kovarian and Manton left . At some point after Amy ' s baby was delivered , Kovarian took her away and had a Flesh duplicate created as a decoy for the Doctor . The duplicate and Amy were " rescued " by Rory Williams . During the battle with the Headless monk s , Kovarian told the Doctor she was " privileged " to have fooled him twice in the same manner and disconnected the Flesh signal , disintegrating the duplicate . ( TV : " A Good Man Goes to War " ) Assassination of the Doctor . She appeared at the Luna University circa 5123 to River Song . Kovarian taunted her over her capture as a baby and her role in the Doctor ' s death . With Silence and soldiers from the Church , she took River and forced her into an astronaut suit with an upgraded weapons system which controlled her nervous system . River was taken to 22 April 2011 and submerged in Lake Silencio to lie in wait to kill the Doctor . ( TV : " Closing Time " ) The assassination appeared to be successful , and River was jailed for killing the Doctor . ( TV : " The Wedding of River Song " ) Alternate timeline . Kovarian was in the Area 52 pyramid in the alternate timeline created by River Song ' s refusal to kill the Doctor at Lake Silencio , having been captured by River and Amy Pond ' s military group and tied to a chair . They had created their own Eye Drive s based on hers to remember the Silence , but as she told the Eleventh Doctor and his companions , the drives gave an advantage to the Silence ; they could electrify them remotely , causing debilitating pain or death . The Silence began electrifying the Eye Drives , including Kovarian ' s . She pleaded with Amy to save her , but Amy took revenge on her for the abduction of her baby by forcibly reinserting her Eye Drive and leaving her to die . Amy remembered this after that reality disintegrated and was conflicted over her actions , although River tried to reassure her that it was an aborted timeline and didn ' t count . ( TV : " The Wedding of River Song " ) Personality . Kovarian was a cruel , malevolent , sadistic , manipulative and psychotic woman who deeply hated and feared the Doctor because she believed that he would bring about the end of the universe . She took terrible glee in his anguish and humiliation . She was willing to use the Doctor ' s friends against him , kidnap an innocent baby and mould the child into a psychopath . She tortured Amy emotionally by kidnapping the real Melody Pond and leaving a Flesh duplicate in her place after instilling a false sense of safety when she purposefully allowed Rory to carry the fake back . Kovarian was callous , showing little concern for her allies . ( TV : " A Good Man Goes to War " ) Kovarian was cowardly and not above pleading for her life , as shown when the Silence turned on her . She begged Amy to save her life , even claiming it was something the Doctor would do . Amy denied her any mercy , telling Kovarian that River Song had " gotten it " from her mother as well as from her . Kovarian ' s incredible sense of self - preservation was probably what motivated her hatred and fear of the Doctor . She occasionally showed a dry , cynical sense of humour as shown by her remark , " Oh God , do I have to watch this ? " during the Doctor and River Song ' s flirtation . She was incredibly tactless , going so far as to beg the people she had damaged and targeted for help . ( TV : " The Wedding of River Song " )