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4) After realizing it isn't John standing over Sam's crib, what do you think Mary's first thought is? Do you think she added the flickering lights and stranger in the nursery together to conclude demons finally? Or when the angels scrubbed her mind in 5x13, did they take it all, hunter past included?
Elle2 - I think Mary quickly put it all together. Her reaction of not calling immediately for John’s assistance, to me, reads that she was still trying to keep that part of her life hidden – so ingrained in her was that training. Also, while the angels scrubbed her memories after events of The Song Remains the Same, I don’t think anything else was touched; I base that on the fact that in Dark Side of the Moon, it’s clear Sam and Dean remember that they had died, but hadn’t remembered coming to heaven and reuniting with Ash. At the end, they were granted those memories of what happened in heaven that time, while prior ones were gone, but all their other memories remained.
Metamorphic Rocks - Well, in Season 2 "All Hell Breaks Loose Part One," Mary did seem to put it all together, because when the Yellow Eyed Demon takes Sam into the past to see the night his mother died, Mary sees the YED and says "it's you," so she did remember him, which means she recalls the deal she made with him in the Season 4 episode "In the Beginning."
Percysowner - I think she remembered her hunter past. I think the angels only scrubbed the memory of Sam and Dean's visit and that the angels wanted them for the Apocalypse. I think once she realized it wasn't John in the room with Sam she put together the flickering lights and ran up the stairs trying to cobble together every exorcism ritual that she could.
Elle - Panic, obviously. After that, only that a stranger is in the house - not that it's a supernatural entity. If she does remember her past life at all, she had not apparent safeguards in place in her home or around the baby at least, in any way. At the same time, she didn't call for help i.e. yell John's name as she runs up the stairs or anything so it's possible she has no idea. Yes, she does apologize in Home to Sam, presumably for the deal that led to Azazel coming in, etc. and I like to think (on reflection) that the long look she gives Dean is in part realization that he's that guy from the future who warned her not to get out of bed - so maybe angel scrubbing wears off after death. I don't believe she had any memory of hunter living between Dean's birth and her death.