The universe consists of 6 distinct areas - 5 mono-coloured continents/demi-planes:~White Plane~, ~Blue Plane~, ~Black Plane~, ~Red Plane~, ~Green Plane~; and the 1 multicoloured floating sky city Aer.

Aer is divided from the Gloaming (what I've taken to calling the collection of the five monocolor areas) by a thick barrier of clouds, leaving it in constant near-dark. The only plane with a consistent light source is ~Green Plane~, which has its own "sun."

So, I think we have this for a timeline:

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the past: Early Aerans deposit Mana Stones on the 5 monocolour planes of Aer. These stones power the Aer city/plane.

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some time later: The dark clouds dividing Aer from the 5 planes form. Life is brought/begins on the 5 planes. The Aerans don't try to explore past the cloud cover because ???? (insert reason here?)

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near-present: The flow of mana to Aer is disrupted somehow (the mana stones are disrupted or something). The sentient life is probably responsible.

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present: The lack of mana is causing Aer to descend (through the cloud cover?) The 5 monocolor planes can now see the Aerans, and vice versa. FIGHT!

How does this sound so far?

I suggested before pitching the Aer attitude something like European countries' empires: they're vaguely aware that there's some sort of life, even civilisation down there, and possibly even occasionally have minor commerce with it, but they don't think it's important, and aren't used to thinking of the monocoloreds as people (devils, plants, etc). Then when draining the mana starts to be a problem for the monocolored's development, a few bleeding-hearts suggest doing something about it, but no-one knows what and no-one wants to give up their cosy cloud existance. Then one of the monocolored nations makes a direct attack on the mana source, and Aer is suddenly in serious trouble and the nation of scholars and aesthetes suddenly lash out, trying to suppress the various monocoloreds before the mana is cut off even more and their cities start to fall from the sky...

@JackV: Ok. I think this diverges from Link's vision slightly, but I do like it.

I think we can reconcile this with the cloud cover by simply saying that the Aerans created the cloud cover so that the Mono planes couldn't see them, because they're so aloof.