Just a bit more info on my AU Amy Pond. After Amy’s second encounter with the Doctor at the age of 19, she was taken captive by Kovarian. Who twisted with her mind so much that now she can’t escape it. After being dumped back on Earth in a comatose, Amy was placed in Leadworth hospital under the supervision of Rory Williams, her then boyfriend. In her unconscious state is where she’s plagued by a multitude of things. 

Dissociative amnesia: an inability to recall important information, usually of a personal nature. When it occurs following a stressful or traumatic event, its cause is considered psychological, not biological. Failure to recall events that occur during a certain period of time is known as localised amnesia, wheras generalised amnesia is a total inability to recall any aspect of one’s life

Depersonalisation disorder: where the person may feel that the external environment is unreal.

This is why, in her mind’s world, she doesn’t believe Rory to be real. She’s aware she has made him up in a way of bringing her comfort. She believes, her whole life has been more or less spent in and out of mental institutions. 

There are two Doctors in her mind’s world. The ‘good’ Doctor, who is the real Doctor trying to break through to her. And the other one is the ‘bad’ Doctor. He is a result of all of the drugs Kovarian had her on, he more or less mocks her and brings up every insecurity of hers. She is living her life through her mind.