Ok, so first, the knights came from this planet where it was a lot like Earth. It wasn't Earth, but it looked pretty much like it, except there were 9 continents, each with powerful rulers that wanted planetary conquest. Our spiral knights came from the technologically advanced one, called Orin. Orin was a really awesome place. There were a lot of giant skyscrapers and flying cars and stuff. Anyway, all the kingdom places got their energy from the moon, mining scelestium power, which was basically the equivalent of crystal energy. So then, while miners were on the moon-like place, some from the tersti kingdom, a magic using place with lots of castles, disappeared. At the next world meeting in the week, the kingdoms' leaders each shouted at each other over who killed Tersti's miners. Finally, the Orin leader stopped their arguing and urged them to continue mining, as it had been discussed that they should stop it. So they continued. In a week, they all had returned to mining, until a large scale attack occurred, where a black cloud trapped hundreds of miners into they're facility, all of them dying. Eventually, the Scelestium planet grew black, slowly becoming filled with the black clouds. Some began to take shape, and energy missiles were launched at the surface of the moon, but nothing changed. Eventually, the cloud swarmed and destroyed all of the kingdoms except for the Tersti kingdom, the Siklior (a kingdom of the undead), the glasc (a kingdom of jelly), and Orin. The black clouds emitted creatures that rampaged throughout towns, destroying hundreds of people. The alpha squad, back then the knights of Orin, fought with hi-tech energy emission beams that could destroy hundreds of the half-life monsters that arose from the muck, but energy supplies were dwindling and their numbers slowly diminished. Tersti and Siklior nearly died off before the Skylark launched from Orin, barely allowing the last few survivors to escape. After fighting off the black cloud creatures contaminating the ship, it was found that the Tersti's truly destructive magic wouldn't last outside of the range of the scelestium moon and that they had used up all the energy possible without taking extreme risks that could end with the skylark being out of gas in the middle of no where. Anyway, the knights struggled to survive, a couple scientists making new proto weapons and armor that would be given to everyone of the knights. Finally the survivors approached a distant planet, but the readings of energy and dangerous lifeforms was off the chart. They tried to turn the skylark away, but an awful giant monster broke through the clouds of the planet, destroying the storage and engines in the ship. The skylark crashlanded, and the knights arrived where they are today. So yeah, that's what happened in my mind. There is another side story for my own knight, but that isn't really relevant to the whole idea of their origin. Oh, and the shadow lairs are traces of the black stuff creeping out of the core, and the knights are destined to fight off the monsters forever.
P.S. The mewkats are awesome.