Fuddlemiff
Is this real life?
I reckon her consciousness is partly in a mental asylum, but maybe the events we are seeing exist in real life at the same time (I don't think they'd want to have a fantastic episode with the Doc talking to the Tardis only to say at the end of the season "oh yeah, it was all in Amy's mind. It never happened".) Maybe she's in two dimensions at once, explaining the weird readings on the pregnancy test.
Or I suppose her thoughts could be altering reality somehow. She's worried about Rory dying, so he dies. She thinks she's pregnant because the Silence made her feel queasy, so suddenly she is pregnant.
Or I suppose her thoughts could be altering reality somehow. She's worried about Rory dying, so he dies. She thinks she's pregnant because the Silence made her feel queasy, so suddenly she is pregnant.