or MCP is actually governed by the three laws of robotics--- wait, he's a program!

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Kind of over-analyzing things man, no offence.
But I'll add my two-cents...

Flynn was converted into energy, yes he's "code" in-a-sense, but in a metaphysical sense he's a living soul/mind as code "soul code" (to borrow a term from Steve Lisberger as of yet unmade film project) exsisting in a microcosmic cyber space dimension

Yes in the cyberspace realm he's a "proxy" a digital approximation-construct of the "real Flynn" i.e. "not any kind of Program... he's a User" as the MCP so clearly stated to Sark.

This sets "digital Flynn" apart from Programs, hence his ability to re-assemble a broken up Recognizer, redirect a beam of energy, suck the energy out of an Elite Warrior Program, or instill energy into Yori to stop her from derezing.
Flynn as "soul code", a living mind in this digital dimension allows for him to have those abilities to manipulate the digital realm in certain ways by will power & thought alone where as Programs cannot. ( The Matrix ripped off these concepts from Tron and Gibson's "Neuromancer"! )

He may *resemble* a Program, but he is not one.
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You seem to not fully understanding what I wrote.

The MCP is matter-of-factly saying "he's not any KIND of Program" "he's a USER".

The MCP did not say "He's User I converted into a Program and is no different from other Programs!"

Flynn only **resembles*** a Program, his "shell" is LIKE that of a "Program", but he's the computer system's approximation of a living human with a actual human MIND, Flynn is "soul as code."

I wasn't saying he's a 3-D polygonal model. The Bit *assumed* Flynn was a Program because he *appears* to be one, it doesn't know he's different, and other Programs don't see past the "shell", they are not seeing that Flynn isn't really a Program.

That shell gives Flynn some program like properties yes, since he's a human proxy entity. However his human Will and his MIND set him apart from all other Programs. Hence the re-constructing a Recognizer and restoring all it's functions, not being derezzed when diverting a beam of energy, etc... These are abilities that NO Program in that realm has.

There's a metaphysical level that deals with how Flynn himself is percieving things and semi-metaphysical nature of that cyber space realm that you seem to not really noticing or understanding.

I think your being too overly techinical and coming in from only a technological view when there's actually some cyber mysticism in how Tron's cyberspace realm looks and partly in it's very nature.

There's a Taoist fable about a man once had a vivid dream he was a butterfly, and to him he felt and experienced what it is to BE a butterfly, then when he awoke he was a man again; the dream was as real as his life as a person. Was he really a man dreaming he was a butterfly, or was the butterfly actually dreaming he was a man?

Is Flynn really a Program dreaming he's a man, or a man in the form of energy, suspended in a quantum entaglement matrix "dreaming" he's in another realm, the ambguity is there. It's all the perception of Flynn, that mind that is experiencing and inhabiting that digital realm.

Flynn: " This isn't happening, he only thinks it's happening..."
Dumont: " All that is visible must grow beyond itself, into the realm of the invisible"... These are very relevant to what I speak off.

I think it's not all wholely technological...

The digitization laser is called "Shiva"...
probably in refernce to the Hindu god the creator & destroyer of the world/universe as refered to by physicist Robert Oppenheimer
as Supervising Scientist on the Manhattan Project he said

"...now I am become Death [Shiva], the destroyer of worlds..."