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
Somehow, Kovarian learned that Amy and Rory had conceived a child while on board the TARDIS. (TV: The Big Bang) During the couple'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's 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 knew; 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 owed the Doctor a debt for helping them; he was gathering an army. Dorium explained that 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 monks, 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)

Kovarian placed a neural block in Melody Pond's head to prevent Melody from ever killing her. (AUDIO: The Furies)

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 Silents 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 (though in fact River had shot the Teselecta in disguise), and River was jailed for killing the Doctor. (TV: The Wedding of River Song)

Second attempt on the Doctor's life
In addition to Melody Pond, Kovarian used her DNA to create multiple Proto-Time Lords. (AUDIO: The Lady in the Lake) While seven of these Proto Time Lords escaped from Demon's Run following the battle, four more stayed with her. (AUDIO: The Lady in the Lake, The Furies) Learning the Doctor had survived his fixed death at Lake Silencio, she devised a second attempt on his life.

Kovarian placed the Proto Time Lord Brooke 1 with the Fifth Doctor as a companion and tasked her with killing him. She failed due to the interference of River Song. (AUDIO: A Requiem for the Doctor) Kovarian met Brooke following the failure at The Bumptious Gastropod, a temporal restaurant, where she had a record of the Doctor dying. Despite many attempts by River to stop them, Brooke and Kovarian successfully killed the Fifth Doctor, taking his body and River to their ship. (AUDIO: My Dinner with Andrew)

Returning to her ship, Kovarian told her crew and the other Proto Time Lords, H-One, H-Two and O, of how Brooke killed the Doctor and the need to continue protecting the universe. As she celebrated her success, she found herself repeatedly beset by the image of the Fifth Doctor, while a captive River warned her about her own myth of the Furies and that they were real. The images were actually the result of River generating a psychic link between her and the other Proto Time Lords. Kovarian later found herself under attack from the Deterrent, a mechanised race created by the many worlds now dying due to the Doctor's death. Refusing to believe she was anything more than a saviour and still taunted by the image of the Fifth Doctor, Kovarian started to lose her mind in the chaos until eventually all her Proto Time Lord children sided with River. Brooke travelled back in time and prevented the Doctor's death while River, H-Two and O captured Kovarian. She was later imprisoned and guarded by H-Two, O and Brooke. (AUDIO: The Furies)

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 Drives 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, in an alternate timeline, the Silence turned on her, electrifying her eye-drive. 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. She was also incredibly tactless, begging the people she had damaged and targeted for help. (TV: The Wedding of River Song)

Kovarian 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. (TV: The Wedding of River Song)

Kovarian was also fanatically devoted to her cause. When confronted with the possibility she might be wrong, Kovarian refused to believe it and continued to insist her plans to kill the Doctor were a necessity to save the universe and many people would be saved as a result. (AUDIO: The Furies)

Her shortsightedness meant that she never considered the consequences of taking out the Doctor too early in his timeline, (AUDIO: The Furies) unaware of the damage it would cause to the universe if the Doctor hadn't intervened in several places in history, (TV: The Name of the Doctor) or that her blunders did more harm than good (TV: The Pandorica Opens) and had to be constantly corrected by the Doctor himself. (TV: The Big Bang. Let's Kill Hitler)

Behind the scenes

 * Kovarian was credited as "Eye Patch Lady" until the mid-series finale of series six, A Good Man Goes to War. Kovarian made appearances in all the stories in this first half except The Impossible Astronaut and The Doctor's Wife. She appeared under various circumstances, only to Amy Pond and always through a gap in a surface that subsequently disappeared. Her appearances acted as a story arc throughout these episodes and even with her name, little, if anything, was revealed about her.
 * Kovarian was to have a cameo in Night Terrors before the episode was moved to the second half of Series 6.
 * According to The Brilliant Book 2012, a book that contains non-narrative information, Kovarian learned unspecified information from Dorium Maldovar. Kovarian later read Colonel Runaway (né Manton)'s report on the Battle of Demons Run before demoting him to janitorial duties.
 * According to Steven Moffat in Doctor Who Magazine #473, Kovarian may have at one time been married to Tasha Lem.
 * In the comedic webcast Stealing Series 9 Scripts, a Madame Kovarian spin-off series was one of the projects Steven Moffat was considering in his volcano lair below 221B Baker Street when Christel Dee broke in.