Madame Kovarian is a mysterious woman who keeps appearing behind a sliding panel in season six. The panel shows up in random places and times, and is only visible to Amy Pond. We finally learn that Amy has been replaced by an artificial duplicate. Amy's mind is being projected into the duplicate's body. This leaves her free to have adventures with the Doctor while her real body is pregnant and trapped in a life support pod. Madame Kovarian's random appearances are the moments in which Amy becomes partially conscious of her true situation.
In the second episode of season six, Amy, in her duplicate body, discovers a little girl's bedroom in an orphanage controlled by the Silence. On the girl's dresser are photographs of the girl and one of Amy holding a baby. This implies the little girl is Amy's future daughter. But these events are occurring in 1969, before Amy is ever born. Therefore convoluted time travel is involved.
At the end of the episode we see the little girl has escaped the orphanage and is loose on the streets. She tells a bum she's dying, and then regenerates just like a Time Lord.
Reasons that Madame Kovarian is the Rani
- Kovarian has managed to abduct Amy right under the Doctor's nose. This implies she is superhumanly clever.
- She is using a sentient being in a breeding experiment. This is the Rani's modus operandi.
- She has no desire to make Amy suffer, but she also has no empathy or regard for Amy's humanity. This is also the Rani's mindset.
- Her ability to project Amy's consciousness into a duplicate body across all time and space, to secretly abduct her from the Doctor's care, and to move her daughter to another era all imply she has access to advanced time travel technology.
- Her ability to impregnate Amy with a Time Lord (or hybrid Gallifreyan) indicate she has access to Time Lord biodata and knows how to manipulate it.
- In 'A Good Man Goes to War' she is attended by loyal soldiers. The Rani has always used servants, human and alien, to enforce her will.
- "Madame Kovarian" anagrams into "Mad Rani Make Ova" - which could be "Makes eggs" or "Makeover" - "Mad Rani Makeover".