Here is my theory on the creation of cradle (fan fictions only, don’t take the plot holes and horrible grammar seriously):
Billions of years ago, a cloud of energy (mist) was gathered somewhere in the universe, eventually this sphere of pure mist energy GAINED CONSIOUSNESS. It begin to think, and like air, which defuses into the space which is available to it through diffusion, this sphere of energy also wanted to spread its essence across the universe in another word, this sphere of energy wanna conquer the universe...

But, fortunately, for the rest of us in the universe, this massive sphere of energy can't move very well. So it begins to materialize layers of earth around it and created a planet (AKA cradle), and this sphere of energy manifests itself into an entity, he called himself-INCEPTRON, and he became a self-proclaimed god to his first creation(like Adam and Eve). But only this time, he created the Almirians, INCEPTRON taught Almirians how to build and craft, in return they worshiped INCEPTRON like a God. But that changed when INCEPTRON requested Almirians to conquer the nearby planets and wipe out their inhabitants. Against their creator’s will, Almirians rebelled and challenged INCEPTRON's authority as a God. INCEPTRON was pissed, as punishment, he created the SWARM, the harvester of knowledge and memories (those black stuff in the shadow layer). INCEPTRON used the SWARM to consume the Almirians and the cities which they lived in, luckily FSC was not severely damaged, but the perish of the almirian legion consumed Vanaduke with guilt; this is probably the reason why he attacked anything that entered his chamber. (He might mistake SKs as SWARM seeds due to his severe delusion)

With his first creation ended up in failure, INCEPTRON decided to create many new species to populate the planet (jellies, wolvers and so on). And for each time a specie reaches the peak of its civilization( jelly king, snarby are the examples of successful evolution), INCEPTRON harvests their knowledge and invention using the all-consuming might of the SWARM and SWARM is able to fabricate and replicate anything it consumed( thus explaining all those void enemies in shadow lair). But still some of those creatures are PRESERVED to serve as a trophy and a comparison with his other creations (ice queen, rabid snarby).

INCEPTRON now uses the harvested knowledge to create better creatures and hoping one day he can create a species that can truly help him to rule the universe. Currently, his latest project is the Gremlins, and INCEPTRON appointed one of its most talented engineer-tinkinzar to be the “architect” and ordered tinkinzar and his people to build the unbuildable, an orbital starship fleet. During the construction, many gremlins died of exhaustion and accidents in the workshop; cannot bear to see his people suffer. Tinkinzar decided to seal INCEPTRON into the deepest part of cradle through making layers and layers of energy absorbing metal barriers. They made 30 (ish) layers of it in hope that INCEPTRON will never ever escape (since every time he tried to break the barrier, a part of his own body is absorbed in to the barrier). And on the top of that, Tinkinzar blocked the final level all of the four elevators with a monster guardian ( shadow lair ) to deter even the bravest of the adventurers( not SK at least ). But Tinkinzar was proven unpopular after he called in a re-renovation of levels of cradles, but he managed to silence his opposition thanks to his crimson order. He reckons that he needs to rule the cradle with an iron fist (thus making him no better than INCEPTRON) to prevent a great evil.

One day, at his solitude, INCEPTRON sensed a surge in energy in the deep space and he realized that SKs are coming into orbit with a space ship (skylark), he realized that only SK have what it takes to break him out of the prisons, he sent an energy surge into space and led to a meltdown of the tearium reactor of the ship engine, yep, our crash landing was not a coincident, it was staged by INCEPTRON all along. And once when enough CEs are deposited into the sanctuary alchemy machine, INCEPTRON will have enough energy to break out and kill us all with his army of SWARM seeds and void creations.

-----INCEPTRON can be the ENDGAME boss for those pros who wants a challenge. He should be the hardest boss in the game, as the best of the SKs confront him in a final battle in the core to decide the fate of this planet.