I keep seeing something along the lines of "Code: Indigo" or some other color splashed along the top of correspondence between characters in the excerpts. It strikes me as a kind of threat or secrecy rating system, but I don't have the chart, so it's complete nonsense to me.

Can anyone explain the color coding or point me towards a chart?

I don't think it's ever presented as a coherent colour coding system or threat scale in any of the possible sources. Vermillion pops up here and there as suitably dramatic, but otherwise... Nah. If you need something like this, use the security clearance colours from Paranoia. That way you can have both coherency and a neat little chuckle for yourself (Indigo? INDIGO? But my clearance is only GREEN. I turn around and run for the nearest confession booth. Failure to do so is treason. Treason is punishable by death. )

a paranoia reference in 2015!?

Truly, there is much to be thankful for this day.

I'm glad I could cheer you up. Fun is mandatory, after all

We do touch upon the subject occasionally - the atmosphere actually lends itself quite easily to a particularly silly interpretation of 40k, and the good folks at FFG are obviously aware of this, as Friend Computer even has a separate planet in the DW setting. And knowing there's a new edition in the works, I'm getting more and more hooked on the idea of doing some sort of a crossover.

Sorry for the slight necro but I've been wondering how other people take (and or use) this as there seems to be a lack of consistency to the different books fluffiness regarding this scale. In Rites of Battle, the section about the Xenos creatures contained in fortress Erioch seems to use a scale which progresses through the Blue/Purple end of a spectrum denoting increasing danger, whereas most fluff reports spaced throughout the book seem to indicate a progressive red based scale for reports of important stuff.

I've kind of put it together in my brain as being a two pronged scale based on both the importance and subject matter of the report.

The whole scale is then based on the visible light spectrum with inclusions of infra-red and ultra-violet for extreme cases.

For classifying present threats of danger within physical locales: green - blue - indigo - violet - ultra violet

For classifying transmitted reports of imminent importance: yellow - orange - red - vermillion - infra red. (with the possible inclusion of crimson somewhere in there)

It ain't canon by any means and I'm hard pushed to find any evidence to support my theory, but I've ran with it and generally use the colors in the fluff for mission briefings. My players get a kick out of being allowed to read (heavily redacted) reports classified as vermillion and knowing they're being drop podded into a Code:Violet area.

I'd appreciate anyone else's thoughts on this matter, even if its to tell me i'm totally wrong and way off kilter.

Excellent work. Sounds better than my crayola method.

It is entirely possible there are multiple threat scales being used. Dark Heresy 1st edition covers an Inquisition scale of threats from Minima to Terminus.

"Dark Magenta" was a clearance level in the old Inquisitor board game (hence the name of the accompanying magazine)