Designing a new cosmology - help appreciated

Based on the replies to this thread I started a while ago, I'm trying to design a new cosmology for my campaigns. I have a rough sketch of what I want, but I could use some help fleshing out the details and filling in the gaps. This is what I have thus far:

*** The Known World (A combination of Prime Material, Shadow and Mirror planes)

The mortal races originally came from outer space (all PC races except the elves, more on them later). Thousands of years ago they found an alien Object. Research showed that this Object was a source of power beyond belief and the studies also showed that this Object was as old as the universe itself. About 15 billion years. They named it the Force Primeval. They harnessed its power to create space faring vessels and mechas (yes, it's going to be a mecha campaign!), thus beginning an interstellar civilization.

A new faction of scholars was formed around the Force Primeval. I have no name for this faction yet, let's call them Divine Spellcasters for now. Using the energy from the Object, as well as their own knowledge about genetic engineering, they started breeding programs that bonded mortals and the force primeval, giving rise to perfected mortals with divine magic powers and higher attributes. These are clerics, druids, etc. Eventually their breeding programs gave rise to the deities. The deities were too powerful to be controlled and started to get out of hand - some go off into the Dream (more on that later), others stay and start influencing the mortal races, directly or indirectly. It seems like deities are somewhat dependent on mortal worship to survive, given their close link with abstract concepts. The faction members don't think they reached the perfect being with the deities, given their limitations. But they're very close. The problem is getting the cooperation of the deities to keep working. Temples to the various deities are created, and the clerics exchange mortal worship and administration of the temples for the cooperation of the powers in their breeding programs. It's a very fragile pact, filled with manipulation and backstabbing from both sides. The Divine Spellcasters still believe they can achieve their Perfect Being, thus beginning a new age of utopia.

Things went wrong when the mortal races had to flee from an unknown threat in the fringes of outer space. The interstellar civilization is scattered across the universe. A new faction is formed around this time. For now I'll call them Arcane Spellcasters, although at this point they still _do not_ possess arcane magic. Initially an offspin of the Divine Spellcasters faction, they were the ones originally responsible for creating the mechas out of the force primeval. They created them to fight the unknown threat, and they also created a vastly powerful and intelligent spacefaring vessel that would take the mortal races across the universe and into safety.

In preparation for their escape, the Divine Spellcasters had reached a very advanced model in their breeding programs, and they named him Adam (he was not a deity, but equally powerful or perhaps even more so). In Adam was contained the genetic material of all the mortal races. Only Adam and a handful of the divine and arcane faction high ups (including most deities) were deemed necessary to start the repopulation in their new home, and these were brought in cryogenic tanks inside the vessel.

This intelligent vessel crash-landed on the moon of a small planet. The planet is where the campaign takes place. The vessel arrived badly damaged, but with the cryogenic and cloning tanks still functioning. Adam served as the base model for the repopulation. He is virtually immortal, although he has to transfer his spiritual essence into new human vessels once the old body ages. They moved from the moon where the ship crash-landed to the planet below (although they could not take the vessel with them, it stayed behind on the moon).

The repopulation was a wild success. Over the next few thousand years, the entire surface of the planet was covered by one gigantic sprawling metropolis, dotted with surviving forests, deserts, mountains and lakes. The natives of the planet - elves, nerra and shadar-kai - had to adapt to the newcomers. This planet is very peculiar in that three different levels of reality exist within it - the physical world (home of elves), the shadow world (shadar-kai) and the mirror world (nerra). They are collectively called the Known World, along with the outer space.

All three levels of reality coexist in the same physical space, yet never touch each other except in points of transition, where you can pass from one reality to another. They're not different planes in the traditional way, but one single plane. One may be walking down a street in the physical reality and walk right past a nerra standing in the mirror reality, and they won't see or touch each other. Moreover, the shadow world is not a "negative" reflection of the physical world, nor is the mirror world a "twisted" reflection. Each one has its own distinct culture, feel and locations, with its own distinct inhabitants and points of interest. However, they fit seamlessly and complement each other. It's all very integrated and the inhanbitants of the Known World take it for granted.

After the deity fiasco and the Scattering, and influenced by the elves of their new home planet, the Arcane Spellcasters offshoot faction take control of the force primeval and split from the main Divine Spellcasters faction for good. They retreat into the Dream (more on that later) to start their own breeding programs from scratch and finally create their line of arcane spellcasters (using the genetic material of elves mixed with their own and the energies of the force primeval). Wizards and sorcerers come into play for the first time. They seek to understand the origins of the force primeval and perhaps ascend to this higher dimensional state beyond the known universe where the force is presumably from.

Meanwhile, a new faction is also formed, the Sons of Adam. They are a younger faction, more focused on the events after their arrival and/or creation in the known world. To them Adam is God, creator of all (or most) life on the world. Adam is perfecting his children, to make them ready for his great exodus. He will take them back to the outer space where they belong and where injustice and suffering won't exist. This planet is a prison and they must escape. But for that they must still face the Unknown Threat, as well as revive the vessel that originally brought them across the universe. In order to revive the vessel Adam will need either the original force primeval or to sacrifice the life force of all (or most) mortal races on the planet in order to channel the energy of the force primeval contained in each individual person. Sacrificing the entire civilization doesn't sound so bad to Adam because he could simply repopulate new planets all over again.

*** The Worlds of Dream (or simply the Dream - a combination of the Ethereal, Inner and Outer Planes)

This is where the bulk of the planes are, home of the exemplars and other strange beings. The planes (or worlds of dream) go in and out of alignment with each other and with the known world. Spells such as planar travel only work in planes that are currently aligned with each other. The Ethereal is the "sea" that connects the known world and the worlds of dream, and it can be navigated with special dream vessels. The Astral _does not_ exist in this cosmology.

Mortals can go there when they sleep and dream, or with magic. When dreaming in their sleep, mortals exist in the Dream in a very insubstantial form, and cannot affect or be affected very much. The running theme in the Dream is that of probability. There is a world (called realm by dream natives) in the Dream for each possible and conceivable version of reality. There's a grotesque abyss where demons run amok torturing the souls of the dead, a world where elves live in underground mines and dwarves sing in the forest, etc. In essence, the Dream is open to infinite possibilities. The mortal races tend to think that the worlds of dream are a figment of their imagination or collective unconscious, created by their dreams and desires, but that is not the case.

The Dream is more primal, a layer underneath the more rough known world. The Known World sits atop the Dream, and in some ways is defined by it. It's as if the Known World is how the Dream would be perceived by mortals lacking the sensorial organs to observe reality in its full glory. The known world is like a rough and limited version of the Dream, but also unique in its own limitations.

But there's more. The ethereal continues after the Dream ends and turns into the deep ethereal. What kind of layer lies underneath the Dream is a mystery. But some theorize that just as the Dream is a more comprehensive version of the known world, so is this mystery layer at the bottom a more comprehensive version of the Dream, and both mortals and exemplars alike would lack the sensorial organs to fully perceive this higher level of reality.

Another faction exists in the worlds of dream: they are the Dreamers. A group of adventurers and explorers who seek to explore the Dream and unveil its mysteries. To them the known world is only a shell that they must break in order to see the truth, and that is the Dream. The same happens with Death: when the body dies, the souls depart to the various realms in the Dream. At least temporarily. Afterwards they disappear, no one knows where they go (ressurection spells only work if used within a time limit).

The Dreamers are led by the arch-devil Asmodeus, former ruler of the Nine Hells. Asmodeus got bored with his existence as the corruptor of souls and decided to leave his realm and go into the known world to fully explore and comprehend this existencial crisis he was going through. He operates a jazz club that also serves as the headquarters for the faction. The Dreamers are also responsible for the creation of dream machines, inventions capable of sending a mortal's soul into the Dream while his body is attached to the machine (not unlike the astral projection spell).

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Ok, this is what I have so far. I doubt many persisted to read all of this, but in case you did, thanks!
I'm looking for suggestions as I said. What is the unknown threat that drove the mortal races away from the depths of the universe? What lies beneath the worlds of dream and the deep ethereal? How can I flesh out the known world and the metropolis to make it an interesting campaign base? What other overarching themes and metaplots can I add to this cosmology? Etc.