The ending was BIGGER for me.... (SPOILERS)
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Ok. so....
it's ends the way it does and I'm scratching my head for a minute computing what I just saw. And the ending got way bigger for me than what I read on here.
Ending: they escape the big vault, go hide away in the islands and he pitches her disk that showed she was labeled for extermination at all costs. Sure, seemed a tad weak....
BUT... MY Brain put THIS into all that.
Back up a bit to the Vault... it is huge and FILLED with billions of data files. We learn our guy invented or sells or something, that mind altering hypnosis technology. We don't know how many decades this tech has been functional. He pulls HER file from that huge vault. What are the rest of the data files in there?? The rest of the population most likely. Everyone. Presidents, doctors, and lawyers too, unfortunately. They could use these files and make anyone into anyone just by putting stuff in the water.
Anyway, I saw it that he just wanted their individualistic lives back, not leaving her essence out there to reproduce, clone and abuse for nefarious purposes. So his stealing the file of her was keeping them from making her, or him, yet again and reusing them.
Kind of a larger, controlling world system, he helped create, he knew was wrong and wanted them out of it. The companies knew it, feared they would destroy their profits, and marked her (and him most likely) for termination.
Anyway, that was my larger intepretation of the ending. And it made sense to me and fit perfectly with the knowns.