Things I wasnt quite clear on about this movie...

I think the problem is less to do with the movie and more to do with the lack of ability to suspend belief. This is not a plot-heavy movie. It's an action flick - it really doesn't have to make sense.

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I really enjoyed this movie. The questions you pose are all good ones, and I’m sure most viewers, at least briefly, thought about most or all of them. I know I did.

While I have no definitive answers, I’d like to throw some thoughts your way, and see what you think. OK?

I think there is a difference between an alias and a cover (short for cover story). An alias can be an alternate name backed up by a different ID, papers, or perhaps a passport or such, while a cover has to be sufficiently detailed that if the original Identity (Say Charly Baltimore) is compromised, she can drop off the grid completely, and assume the cover identity. It would have to be a real place, with a very different identity (like a teacher). Waldman told her “You wrote it,” and not knowing exactly what her amnesia situation was, said you bought your own cover. Perhaps her conscious mind had to “grasp” that comforting identity for the sake of sanity. You have to give me a little leeway here.

When she washed up on the beach, she had no ID, just a key filed blank.

Samantha said the doctors told her that she was diagnosed as having focal retrograde amnesia. I looked it up and it is basically where memory for past events and personal information is lost, while the ability to remember new events is spared. So, if she had textbook focal retrograde amnesia, or as you mentioned, the psychological condition dissociative fugue, she would have no knowledge of anything that happened before she was shot in the head and fell off the cliff into the ocean (Which, by the way, would have been enough to “take out” the average person, but there are a rare few – like Charly Baltimore and Jason Bourne – who are able to survive such events). But that wasn’t the case. She seemed to remember a few things (not a textbook case of either condition).

Let’s say that her brain “protected her” by blocking out that terrible experience that her conscious mind couldn’t cope with at that time. However, as her mind searched for something to latch onto, the cover that she wrote filtered through, because it was “something” that her mind (in such a fragile state) could cope with at that time.

And later, something else happened! Her Charly Baltimore identity began to rise to the surface of her consciousness. In her dream, after the automobile accident, the image in the mirror said “I’m coming back. You know that don’t you. By the way, name’s Charly. You are going to LOVE me”

Why was Charly so suspicious of Perkins after the one phone call? Good question. I thought she trusted him. As you mentioned, at that point in time, she hadn’t yet seen any connection between him and that horrible Timothy or Daedalus.

Maybe being in her full Charly Baltimore spy mode (with double agents and all of the deceit in her line of business), and just knowing that people were trying to kill her, she was suspicious of everyone. But, why Perkins in particular? She knew Perkins well, because she subconsciously named Caitlin’s little bear Mr. Perkins. Perhaps she just didn’t trust him in general. Or, this may have been just one of the many things that one just had to "overlook" to enjoy the story.