First of all, I believe that Lego, or at least Farshtey, intended the universes of Bionicle and Herofactory to connect. I don't know if others have proposed this, but this I believe is the best possible connection, and the one I believe Farshtey intended.
Makuro is one of the great beings.
During the Core wars, he left his planet in search of a renewable source of energized protodermis and a haven from Annona's powers.
He desired to create a robot army that could defeat Annona, as they would be resilient to mind attacks.
He found Quatros, an energized protodermis enriched planet, that's why it falls apart (like Spherus Magna) when the quaza is removed.
He created a society built from robots. His AI system was so advanced, the robots were sentient.
He powered the robots with Energized Protodermis, also known as Quaza.
Eventually, he stumbled upon an ultra-powerful design: Implanting a core of solid quaza into the robots' bodies. At the same time, he noticed that crime among his own robots was growing at an alarming rate.
He created Hero Factory: A police force for his robot universe and a way to test the effectiveness of his new Core-implanted robots in action.
He finally had a design he thought would work: Thresher.
So he told Thresher everything: About the original planet Spherus Magna, the core wars, and his quest to defeat Annona.
Thresher went to fight Annona, Makuro's old nemesis. It was an experiment in mind protection: Robots have no “brains” only computers.
The quaza, or energized protodermis, mutates Aldous Witch when he powers himself with it.
The animals on quatros are obviously rahi.
The doom box was created by four great beings, one of whom is eventually killed.
Black Phantom and Voltix may be Dark Hunters, but this is unknown.
This all works with, and is in fact supported, by the Hero Factory Canon. What do you think?
First of all, I believe that Lego, or at least Farshtey, intended the universes of Bionicle and Herofactory to connect. I don't know if others have proposed this, but this I believe is the best possible connection, and the one I believe Farshtey intended.
Makuro is one of the great beings.
During the Core wars, he left his planet in search of a renewable source of energized protodermis and a haven from Annona's powers.
He desired to create a robot army that could defeat Annona, as they would be resilient to mind attacks.
He found Quatros, an energized protodermis enriched planet, that's why it falls apart (like Spherus Magna) when the quaza is removed.
He created a society built from robots. His AI system was so advanced, the robots were sentient.
He powered the robots with Energized Protodermis, also known as Quaza.
Eventually, he stumbled upon an ultra-powerful design: Implanting a core of solid quaza into the robots' bodies. At the same time, he noticed that crime among his own robots was growing at an alarming rate.
He created Hero Factory: A police force for his robot universe and a way to test the effectiveness of his new Core-implanted robots in action.
He finally had a design he thought would work: Thresher.
So he told Thresher everything: About the original planet Spherus Magna, the core wars, and his quest to defeat Annona.
Thresher went to fight Annona, Makuro's old nemesis. It was an experiment in mind protection: Robots have no “brains” only computers.
The quaza, or energized protodermis, mutates Aldous Witch when he powers himself with it.
The animals on quatros are obviously rahi.
The doom box was created by four great beings, one of whom is eventually killed.
Black Phantom and Voltix may be Dark Hunters, but this is unknown.
This all works with, and is in fact supported, by the Hero Factory Canon. What do you think?
I really like this theory. It makes a lot of sense. The beings who created the Doom Box were reptilian, but then again, I don't think the Great Beings were ever explicitly stated to be mammalian anyway. Another thing I could add to this, is that maybe Fire Lord and the other fire powered villains in his group got their powers initially from the Element Lord of Fire, perhaps, who learned about Makuro's robot colonies, and wanted to gain a foothold in them?
Who is Thresher, though? Is he a canon character? It's been a while since I've read/watched Hero Factory's story, so I don't remember that character.
Thanks! Thresher is the leader of the original Alpha team that Stormer and Von Nebula were a part of, according to HeroSector01: HeroSector 01 | Thresher
Everything I read about him on Heropedia seemed to confirm this theory, at least indirectly, and nothing contradicted it
Thanks! Thresher is the leader of the original Alpha team that Stormer and Von Nebula were a part of, according to HeroSector01: HeroSector 01 | Thresher
Everything I read about him on Heropedia seemed to confirm this theory, at least indirectly, and nothing contradicted it
The brains are probably just mutant Krana. (I think those are the Makuta worms! ) Maybe Von Nebula got help from a Makuta?
Did Von Nebula make the brains?
That's another really popular theory. The shadowy person at the end of Breakout is obviously the guy who made the brains in Brain Attack, and it's very likely that Von Nebula was that person, since Voltix broke Von Nebula out of his staff at the beginning of Breakout.
Mr. Makuro isn't tall enough to be a Glatorian, which, the Great beings were Glatorian.
Ah, but sizes in the Hero Factory/Bionicle universe change. For example, by the end of G1, matoran were the same height the toa were at the beginning. It's just the building system though, in-universe Makuro could be the same height as a glatorian.
Another thing I could add to this, is that maybe Fire Lord and the other fire powered villains in his group got their powers initially from the Element Lord of Fire, perhaps, who learned about Makuro's robot colonies, and wanted to gain a foothold in them? 
) Maybe Von Nebula got help from a Makuta?
