Kovarian

Madame Kovarian was an enemy of the Eleventh Doctor, associated with the religious movement, the Silence, an academy of the Question. She wore an Eye Drive over her right eye, which allowed her to remember the "memory-proof" aliens who ran the Silence. Kovarian remains a mysterious figure and for reasons unknown was desperate to destroy the Doctor.

Biography
Some time after Amy's honeymoon, Kovarian arranged her abduction and replacement by a Ganger. Amy's real body was taken to Demon's Run in the 52nd century. Kovarian watched over her through a hatch above the room she was being held in, while her 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 how the pregnancy was going. (DW: A Good Man Goes to War)

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, but Kovarian ignored her and said "No, I think she's just dreaming", then disappeared. When Amy entered, the room appeared to be empty, with no evidence of Kovarian or the hatch. (DW: Day of the Moon)

While asleep 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" and vanished along with the hatch. (DW: The Curse of the Black Spot)

She was seen twice by Ganger Amy at an acid mining factory, the first time 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. When she mentioned this to the Eleventh Doctor, he dismissed it as "time memory, like a mirage." (DW: The Rebel Flesh / The Almost People). 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. (DW: The Almost People)

After Amy's baby was delivered, Kovarian took her away and had a Flesh duplicate created as a decoy for the Doctor. The duplicate was 'rescued' along with Amy 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. (DW: A Good Man Goes to War)

Kovarian appeared at the Luna University circa 5123 to River Song and 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 the same astronaut suit she was put in as a little girl, which controlled her nervous system. She was taken to 22nd April 2011, and submerged in Lake Silencio, lying in wait to kill the Doctor. (DW: Closing Time)

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 militia group and tied to a chair. They had created their own Eye Drives based on hers in order 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.

Personality
Kovarian was a cruel, manipulative and sadistic woman who deeply hated and feared the Doctor for reasons unknown. She took terrible glee in his anguish and humiliation. She was willing to use the Doctor's friends against him and kidnap an innocent baby and deliberately make the child into a psychopath. She tortured Amy emotionally by kidnapping the real Melody Pond and leaving a Flesh duplicate in her place. Kovarian was very callous, showing little concern for her allies. (DW: A Good Man Goes to War)

However, she was 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. (DW: The Wedding of River Song)

Behind the scenes

 * Kovarian was credited as "Eye Patch Lady" until the mid-season finale of series six, A Good Man Goes to War. Kovarian made appearances in all the stories in this first half besides 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.
 * Although it was made clear that the alternate timeline no longer existed, it was not specifically made clear whether or not Madame Kovarian was alive again afterwards. (DW: The Wedding of River Song)