Bionicle/WMG

Spherus Magna is a post-Beast Machines Cybertron
The energized protodermis being came from the core of Spherus Magna, the homeworld of the Great Beings/Maximals, telling the story of how the planet had been ravaged by war over the precious resource that was the energized Protodermis that made it to the surface. Energized protodermis itself was the substance that caused the whole reformatting, considering a technorganic conversion was part of the planet's destiny as a whole. Some time in the future, energized protodermis made it back up to the surface, sparking the war as a result of further study of its mysterious and powerful properties.

Cybertron being the home planet of the Great Beings would also explain why their creations themselves are essentially technorganic Cybertronians, what with the similarities to sparks and heartlights, the transformation abilities the Makuta and Krahka possess, or combining that occurs within the Matoran race.

-on that note..

Spherus magna is pre-war within Cybertron
Think about it. The designs of Bionicle look a lot like early protoforms, and would seem like the early work of Prima (look it up on the Transformers Wiki). also, many Bionicle characters and factions share similarities to transformer counterparts (order of Mata Nui/children of Primus, brotherhood of Makuta/minions of Unicron, Autobots/Toa, Decepticons/Dark Hunters).
 * Not...not really. Especially not on the Decepticons being comparable to the Dark Hunters. The Dark Hunters don't want to destroy everything and take over the world - they're merely mercenaries, and take jobs from their boss based on their abilities. They do what the job entails, and then return home to count their money. They're more Chaotic Neutral than Chaotic Evil. A more accurate comparison might be the Brotherhood of Makuta to the Decepticons, but even that is seriously pushing it.

The Energized Protodermis Entity is the real Big Bad.
It caused a civil war, and the Shattering, on its own. It was there when Makuta was doing his experiments (who knows what it could have told him?). This is just the logical next step.

The Rahi from Dwellers In Darkness chapter 3 was King Ghidorah
"It erupted from below ground in a shower of rock and earth. Well over 60 feet high, it scanned the battlefield with its three heads. Muted light from the sunholes reflected off its brown scales as it spread its batlike wings. Its cry of triumph shattered crystal structures as far away as Ko-Metru."
 * Ghidorah is more gold than brown. That fella really needs to take a bath.

"Axonn" isn't a Punny Name, rather, the opposite.
He's so old that he invented the axe and named it after himself.

Malum and Strakk had a Batman Gambit going with the goal of Screw This, I'm Outta Here
There's a line in "The Crossing" that mentions that they were friends. So why would Malum try to kill Strakk?

Simple—so he could have an excuse to abandon ship before the Skrall killed everyone.

They figured out that They also figured that nobody would believe them if  so they decided to escape.

First, they wait for an opportunity. Once they wind up in the same match, whoever won would try to kill the loser, counting on other Glatorian watching (or whatever) to stop him. After that, Strakk waits for a similar opportunity (such as the fight with Ackar in the movie) to get himself fired. Whether Ackar lived or died didn't matter to Strakk because he's a Jerkass.

Malum is dead
He was killed by Stronius, a turncoat Vorox, or Mata Nui's landing.

Spherus Magna is Earth in the distant future.
In millions of years, after the biological lifeforms have died off, Earth will return to the way it was before we came along and ruined it. The Great Beings will come by in the search for more Energized Protodermis, and the Great War shall begin, eventually resulting in the planet splitting according to the three ecosystems of desert, ocean, and jungle.

And so the story begins.

The Great Beings are giant Lego Mini-Figs
They have a thing for building and creating, and it would be a wonderful twist.

The Great Beings mentioned so often are humans
Sometime in the future, a group of humans is forced out of our dimension by some catastrophe, and escape into a dimension which they created. thus, when they found themselves alone in this universe, they used their control over it to create all the worlds on which the Bionicle cast lives.
 * Jossed. [ MULTIPLE TIMES ]

Mata Nui was actually a Seed of Life, similar to Adam and Lilith in Neon Genesis Evangelion
The Great Beings would then also be the First Ancestral Race.

The Heroes of Hero Factory are in fact creations of the Great Beings.
They were built before Mata Nui and sent into the galaxy on a terraformed asteroid. The Great Beings forgot about them when Mata Nui was launched, and they built their own society.

The Bionicles are some form of nickel.
Why? Listen to the name. Bionicle. Prounounced. Bi-o-ni-kel. So... they are... biological nickel.
 * Jossed. "Bionicle" means biological chronicle.

The Great Beings are actually the Forerunners
Think about it. The Forerunners left our galaxy some time ago. Let's say that they moved to Spherus Magna, where they set themselves up as Scientist-Kings. And that planet that Master Chief is floating towards at the end of Halo 3? Spherus Magna. This just screams for a Halo/Bionicle crossover: Maybe, Halo: Bionlogical Chronicle'. Or perhaps, "Bionalo?"
 * The Borohk are a low-resource form of Sentinel, and Mata Nui was built to scout out the rest of the universe for Flood. The reason that Mata Nui has complete control of his internal environment and the ability to jettison materials is so that any flood infestation that gets inside can be contained and the expelled.

Mata Nui is a relatively small Tengen Toppa Gunman.
Seriously, he's a robot that is several million feet tall and contains a world. What else could he be? The Great Beings, therefore, are the first Spiral Race.
 * Well it would be more like a Cathedral Terra type Gunmen
 * He could just be a prototype - more energy-efficient to build a planet-sized mecha so you know if it works before you go onto a galaxy-sized one. Are there even any Cathedral Terra-types other than Cathedral Terra/Super Galaxy Gurren Lagann?

The Hero Factory series takes place before Bionicle.
The Heroes will fail to prevent some calamity, which will split their world into the Bara, Aqua, and Bona Magma spheres. The robotic populace, upon the failure of their heroes, will put all of their resources together to create Mata Nui and its inhabitants, leaving one of the former Heroes to rule as the Great Spirit.

The Hero Factory series takes place after Bionicle.
With the Mata Nui robot destroyed, any Matoran-creating facilities are out of commission. The Matoran spread out across the galaxy in search of the Great Beings, but their search is unsuccessful. Whether the Great Beings are dead, or hiding in shame, or what, they can't or won't help the Matoran. As the Matoran population wears out, becomes Toa, or dies, they create fully mechanical robots that can more easily replicate to replace themselves; as the Toa population dwindles too, someone (probably Nuparu) gets the bright idea to create the Hero Factory, modelling the Heroes after Toa and using Quaza as a heart-light imitation slash battery. Akiyama Makuro might well have been the last Matoran-made robot, created specifically to head the Factory, and is likely the only robot alive who remembers the robots' Precursors.

The Tatorahk knows The Question.
This is why it continuallu asks for The Answer
 * Looooooooong since jossed, the answer he wanted was how he got transported to Metru Nui from his home island.

Vezon is obfuscating his insanity.
He acts like a Cloudcuckoolander, but that's because he'll be taken less seriously and viewed as less of a threat. He's really still just as creepy-insane as he was back on Voya Nui, he's just smart enough to hide it.

Spherus Magna will become Planet U.
After some enormous calamity that wipes out the majority of the surface population, what little remained of Spherus Magna's life-forms were forced to migrate underground, into the caverns that had been hollowed out by the exttraction of Energized Protodermis. All that remained of the mutagenic substance were energized crystals. Naturally, the Skrall were the most suited for this kind of life, and with the artificial acceleration of the Energy Crystals they split into three distinct tribes suited for life in different parts of the crust, forgetting about their origins.

The Great Beings are the Xel'Naga of the Starcraft universe.
Really throwing things around here. Actually, all prehistoric celestial beings are of the same species. They just split and created different things - The Great Beings created various robotic creations (i.e. Matoran), while the Xel'Naga.

The Energized Protodermis Entity created humans.
In the serial "Destiny War" there are certain creatures described in Chapter 7: "short, pale bipeds with large eyes and spindly arms and legs." Sound like anything we know?
 * The chapter says "large yellow eyes'', quite uncommon among humans, 'FAIK. Since when are large eyes of any color indicative of us anyway?