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I had heard about this color switch before, and here's a quote from Wikipedia article about Tron.

The original script called for "good" programs to be colored yellow and "evil" programs (those loyal to Sark and the MCP) to be colored blue. Partway into production, this coloring scheme was changed to blue for good and red for evil, but some scenes were produced using the original coloring scheme: Clu, who drives a tank, has yellow circuit lines, and all of Sark's tank commanders are blue (but appear green in some presentations). Also, the light-cycle sequence shows the heroes driving yellow (Flynn), orange (Tron) and red (Ram) cycles, while Sark's troops drive blue cycles; similarly, Clu's tank is red, while tanks driven by crews loyal to Sark are blue.

I could understand there was some political concern around this switch, the red color being traditionally associated with Soviets and blue with Americans. But I couldn't find any reference to it.

But, why did they do that? And who made this decision?

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    There's also a certain amount of "red are the bad guys" in video games, though it's impossible to say if that's the reasoning behind it. – thedaian Jan 10 '12 at 17:39
  • I always figured Clu was just a random color, before the "good and bad" sides of the computer world has really been delved into yet. The inverse bike colors though always did puzzle me (which they "fixed" in TRON: Legacy). – eidylon Jan 10 '12 at 18:14
  • Colour-Coded For Your Convenience: Tron red/blue coloring seems to line up somewhat with lightsaber coloring, but is opposite to G.I. Joe laser coloring. – gnovice Jan 10 '12 at 18:18
  • @eidylon But Tron Legacy took place on The Grid 2.0, so Flynn was able to make the colors anything he wanted. Apparently he just really liked the non-color white (as evidenced by where he lived in the Grid) and so the second time when he got to pick his color he took white first. – Xantec Jan 10 '12 at 18:20
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    @gnovice Darn you for not putting on a tvtropes disclaimer. – Xantec Jan 10 '12 at 18:22
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I can't find anything about why the colours were changed during production - it could be that they hadn't completely decided on a scheme until after some scenes were already coloured. The cost of rotoscoping the circuitry over the actors would likely have prohibited going back and fixing it again. However, I can't find a sequence of work to confirm the order in which scenes were rotoscoped - although, I'm pretty sure I read somewhere that the light-bike sequence was one of the first scenes to be drawn up since that would then become the proof of concept for the rest of the work (plus being a pretty cool sequence to sell the rest of the movie to the producers).

The Tron wiki does have more details about the various colourations (in the original and sequel, as well as 'canonical' expanded universe), and provides some extra classification of the programs.

Interestingly, CLU is yellow because he is a search program, the MCP tankers are green ('military') - the blue probably being an error/early colour.

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Super late on an answer but I have one that "must" be the reason... Red has always been associated with "bad" in media/storytelling... Satan, Siths, red eyes for bad guys throughout storytelling history, etc..

Makes sense that they changed it, it would have been weird, I think, because of the historical associations... (I would normally not, myself, associate anything with anything, exclusively, like that. I think the color red might, actually, be the only color or thing I can think of that I would specifically associate with "evil".... not that red equals evil, but that green, blue, orange, etc, would not "signify evil' to me, had they been dressed in it, if that makes sense.

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    This doesn't explain why the scheme changed between films – Valorum Jul 26 '15 at 11:46

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