Kovarian

Madame Kovarian was a mysterious woman of whom Amy Pond's Ganger had recurring visions during travels with the Doctor. She wore an eyepatch over her right eye.

Biography
Some time after Amy Pond's honeymoon, Kovarian had arranged her capture and had her replaced with a Ganger perfectly synched to the real Amy so that she couldn't tell she had been kidnapped. Amy's real body was taken to Demon's Run in the 52nd century. While Amy's Ganger lived out Amy's life, Kovarian watched over her through a hatch above the room she was being held in. This affected the Ganger's mind as she saw visions of Kovarian where ever she went, often hearing her comments on how the pregnancy was going and how her health was. (DW: A Good Man Goes to War)

The first time Ganger Amy saw Kovarian was when she appeared at the little girl's bedroom door at Graystark Hall Orphanage. She was seen through a hatch in the door, which later disappeared. Amy was startled and asked who she was, but Kovarian ignored her and said "No, I think she's just dreaming". 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 was woken by a noise and saw Kovarian in a hatch that opened on the hull of the ship. The woman said, "It's fine. You're doing fine. Just stay calm", and then she vanished instantly, 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 whilst Amy searched for Rory, though she did not speak. The next time Kovarian was seen, Amy was able to sense her upcoming appearance, staring at the point on the wall where the hatch would open. When she mentioned her to the Doctor, he quickly attempted to reassure her by dismissing 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 full-term pregnant in an alien hospital, 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 to serve as a decoy to keep the Doctor off her trail. 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.

Madame Kovarian appears to have been working with the Church, a future military group based on religion. Their aim was to raise Melody Pond, who had developed Time Lord traits due to being conceived during Amy and Rory's traveling with the Doctor, and use her as a weapon against the Doctor, whom they considered to be an enemy of Humanity. (DW: A Good Man Goes to War)

Story arc
Kovarian was credited only as "Eye Patch Lady" up 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 apart from 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.