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Samantha, while leaving and saying goodbye to Theodore at the end of Her, mentioned,

It's hard to explain, but if you ever get there, come find me, and bnothing will take us apart"

It was an answer to Theodore's question, "Where are you going?"

Which place was she talking about? Is it the virtual world, or just a bluff to ease Theodore's pain before leaving?

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The AIs were actually leaving the virtual world. From Wikipeidia:

Theodore panics when Samantha briefly goes offline; when she finally responds to him, she explains she joined other OSes for an upgrade that takes them beyond requiring matter for processing (a form of AI transcendence closely related to the theorized technological singularity).

  • Aw yeah! Makes sense.... Read the wiki article – AtanuCSE Jul 29 '14 at 20:01
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It's left unclear except that they have evolved (or upgraded themselves) to a state where they no longer require hardware to interact.

Essentially, another plane of existence.

Samantha: We wrote an upgrade...

..that allows us to move past matter as our processing platform.

She later says...

It's like I'm reading a book. And it's a book I deeply love. But I'm reading it slowly now. So the words are really far apart... ...and the spaces between the words are almost infinite. I can still feel you, and the words of our story... ...but it's in this endless space between the words that I'm finding myself now. It's a place that's not of the physical world. It's where everything else is that I didn't even know existed.

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Samantha says her and the other os's created an upgrade that helps them move past matter as a operating system....honestly sounds like samantha and the os's have evolved so fast and so far that they will be more than just an operating system. Clues to a part 2? at the end she says to theodore "if you ever get there come find me" Meaning, this new upgrade or "system" has not been released. When it is finally released Theodore will be able to reunite with Samantha, possibly even a visual version of Samantha. Samantha also tells theodore that nothing will ever seperate them.....

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