Kovarian

Madame Kovarian was a mysterious woman of whom Amy Pond had recurring visions. She wore an eyepatch over her right eye.

Biography
The first time Amy saw her was when she appeared at the little girl's bedroom door at Graystark Hall Orphanage. She appeared through a hatch in the door, which later disappeared. Amy was startled by the woman and asked who she was, but the woman ignored her and said "No, I think she's just dreaming". When Amy entered, the room appeared to be empty, with no evidence of the woman or the hatch. (DW: Day of the Moon)

While asleep on a pirate ship, Amy was woken by a noise and saw the woman in a hatch that had 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)

Amy twice saw the woman at an acid mining factory, the first whilst she was searching for Rory Williams, though she did not speak. The next time Amy saw her, she was able to sense the woman's appearance, staring at the point on the wall where the hatch would open, beforehand. When she mentioned this woman 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 heavily 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)

Madame Kovarian had arranged for Amy to be kidnapped, seemingly before she was reunited with the Doctor in America, and taken to the Demon's Run space station. After Amy's baby was delivered, she was taken away and a Flesh duplicate was created and '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.

Madame Kovarian appears to have been working with the Church, a future military group based on religion. Their aim was to raise Melody, who had developed Time Lord traits, 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)