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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Shades of Grey
The Riff Raff are the real future humans. Homo Coloribus are the result of extraterrestrial and human crossbreeding.
  • Point 1: The Riff Raff seem to see at least more than one color and aren't affested by artificial colors (or at least it seems that they can't get the Mildew), like us.
    • RiffRaff can get the Mildew, there's a mention of some captives that did (most captives do, it's implied). It might have been a lie, like most things concerning the Mildew, but it makes just as much sense that it's technically true that they caught it.
  • Point 2: The Riff Raff refer to themselves as "The Digenous" as in indigenous, which means something along the lines of "the original inhabitants." If they (or their ancestors) considere(d) Homo Coloribus invaders, this name makes perfect sense.
    • Alternatively, by crazy etymology, "The Digineous" could mean the opposite to indigenous, and they're the outsiders.
  • Point 3: The whole "invaders" angle also gives them good reason to hate Homo Coloribus the way they do.
    • Do they really hate Homo Coloribus? The only ones we actually meet seem not to go much beyond dislike, and most of the what we hear about the Riff Raff is probably just propaganda.
      • Jane seems to think so. And it's not like they don't have plenty of good reasons to, the Collective hoards all the good land and Previous artifacts they can get their hands on, forcing the RiffRaff to scrape a meager existence in the wilds (which are infested with megafauna and yateveos, the latter of which was specifically created by the Collective to kill RiffRaff!)
  • Point 4: The author even hints at in in this article. He says in the section "Colour Vision Deficiencies" that the fact that everyone can only see one color is near impossible in modern humans, leading one to "consider that Eddie and his kind are not like us at all." The colorblindness could be the result of a genetic defect caused by extraterrestrial and human DNA combining.

The Something That Happened was an alien invasion.
You heard it here first.

The offspring of people of complementing colors are no longer colorblind.
This is why people of complementing colors are forbidden to have children: Once someone sees all color naturally the Head Office has no control over them.
  • Alternatively, that is where Ultra-violets come from.
    • Jossed. Ultraviolets are just very highly-perceptive Purples.

Additionally, the offspring of people of complementary colors are immune to the Mildew.
We know that people who see colors naturally are unaffected by the artificial colors that affect other people (natural Greens can't go to the Green Room when they're struck by the Mildew (as mentioned in the chapter 'One Eyebrow')). We also know that The Mildew is a color, a "greeny-red." So any children of complementary colors would not only be able to see all the colors, they also would naturally see green and red, and thus they would be immune.

The Shades of Grey universe is the future Pokémon universe
You read it here first! Cities in this universe have similar or identical names to those in the first-generation Pokémon games (Vermillion, Cerulean, Cinnabar), and the wilderness around them is populated with strange animals, all of which have (apparently) naturally-occurring barcodes somewhere on their bodies, taxa numbers that once upon a time would have been used to log them into the Pokédex.

It's all an experiment run by Friend Computer
You want a reason? Well, only being able to see the colour of your Clearance Level would stop people going into areas higher than their clearance. Now please report to the nearest Termination Booth for questioning Friend Computer's reasoning.

Holden Russett is secretly working for Head Office
Jane mentions late in the book, that swatchmen are generally lackeys for Head Office, infecting unruly citizens with the Mildew. Although she believes that Holden is not an evil man, it's entirely possible that he is edging Eddie on, pushing him forth into situations where he will either be captured by agents of Head Office or inadvertently reveal pertinent information to them about the resistance. After all, it takes a pretty shitty dad to set up his own son to be raped.
  • But that's kind of the point - the society is so messed up that even a reasonably decent man will do something that unpleasant. Pimping out your own children is endemic.

The Colourman is Eddie's father
As shown in the end, Eddie's dad is not his dad at all. So, the only person introduced to be high enough on the red is the Colourman, and he says that he is somewhat 'related' to Eddie. You heard it here first!
  • This was something I thought as well, going through the book. Matthew Gloss' actions can be seen as creepily paternal, particularly offering Eddie the opportunity to join National Colour.

The main characters are all robots, the Riff Raff are the remaining real humans
The Something That Happened was the robot revolution. The robots all had a massive sense of inferiority over the fact that they were not real creatures, Munsell's Epiphany was that if the robots did not know they were robots then they were free to live happy lives. The point of the Leap Backs is to bring science so low that no-one can even comprehend the idea of what a robot is. This is how everyone has a bar code and how they can have programmed responses to colours and sounds.
  • That seems very unlikely, given that they can reproduce and everything. Artificial Humans, perhaps, but Ridiculously Human Robots seem unlikely, especially given the fact that the Bestiary on the website does show some genuinely robotic 'animals' such as the Asimov Horse.

The original humans invented space travel and left Earth. The people who were left behind have been subject to intense genetic alteration and/or testing.
Jane specifically mentions the "lights on the dark part of the crescent moon," which apparently look like stars. These seem a lot like moon bases. Taken into account with the other lights that streak across the sky, some of which are probably meteorites, some of which might be satellites, and others of which might be space stations, you get what a spacefaring civilization might look like to an earthbound human...ish. Perhaps the Fallen Man was meant to be looking in on the remnants to see how they're doing when his lander failed or something.

Homo Coloribus and indeed the entire Collective are a huge experiment to test something unknown or a bizarre future theme park, perhaps both.
It would explain all the limitations on space and population that the citizens have to deal with, as well as the strict adherence to the seemingly arbitrary Rules. The barcodes on everything can be explained as the people running the show wanting to keep track of everything in their mock environment. The line about giant swans flying so high they sometimes don't seem like swans suggests that they are planes doing fly-overs of the environment and the Fallen man who seems to be a pilot who didn't eject safely supports this. Then of course the bizarre limits on a Collective citizen's vision, their differing appearance to modern humans and their heavy lifelong condition suggest heavy genetic alteration. This doesn't really explain the presence of Riff Raff though.

Homo Coloribus is the result of nanotech wired into the nervous system.
The effects of certain colors, causing mild hallucinations or acting as an anesthetic, might be possible to implement using pure biology, but the "Herald" which appears during the Gordini Recalibration seems too complex to be something implanted biologically—it's a complete set of visual and auditory stimuli which are apparently exactly the same for each individual. The Previous seem to have some command of nanotech, based on the Perpetulite and the Mildew, so maybe that's how it's accomplished: nanites attached to the eyes or optical nerve interpret certain specific colors as commands to perform certain functions (numb parts of the body, cause hallucinations, enable night-vision, disable the Mildew response.) The Herald is a feedback mechanism, letting someone know that their nanites have received input and that they're working—sort of like an "Installing updates. Please do not turn off your computer" message, but for your central nervous system.
A Series of Unfortunate EventsWMG/LiteratureThe Shadow of Black Wings

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