Sorry it has been so long since I've posted. I have been super in real life with work and such, I only have time for one or two drawings a week. What follows is a pitch that might be a bit outdated, but I think still holds up. Keep in mind this is my own head canon, so it branches away from the cast's canon quite a bit.
After Makuta's banishment, he lived out the rest of his days withering away in his mortal form. During his time alive, he was an instigator of countless wars, puppeting the matoran into needless bloodshed. He met his demise at the hands of the last Toa, who slayed the mad tyrant once and for all. There were no tears or ceremony for Makuta, his body was left to rot where he fell.
Origins of the Brotherhood
Two sisters, known only as the Bahlrag, happened across Makuta's remains. The Great Mask of Control took sway over them, filling them with the knowledge and wisdom of the Makuta. They took the mask across the Island, indoctrinating Matoran where they gained entrance. One by one, the mask took hold of them. They longed to see Makuta wear it again.
The Makuta Brotherhood had many unnatural practices, dark magics and sorcery. Artifical Kanohi masks, hybrid Rahi, spellcasting; they turned a blind eye to morality in order to achieve their goals. For years they schemed, planned and honed their skills. Rumours of an ancient mask of power that could null the matoran's defeneses circulated- the Mask of Time.
The Rahkshi are one such a hybrid, the culmination of all the Matoran's spellcasting. Only they could wear the great Kanohi mask of Time, a shattered relic form a time long past. Armed with weapons and wit, the Rahkshii hunted for the scattered shards of the mask.
The Nuva Symbols
After collecting the mask of time, the Rahskii channeled it's temoral powers to place the mainland in a frozen state. Vast cities stood still, defenseless. In the heart of the great capitol cities were the Nuva symbols, ancient relics of creation and the source of each regions element. Save for unexpected return of the mythic toa, the Rahkshi could stroll in and take the symbols.
This is a completely original concept on my part, with the help of @Phoenix. Cryoshells, or Nautali, are how Matoran reproduce. The large metallic chambers are relics or creations, given to the mortal matoran my Ekimu to further their kind. With a donation of elemental energy from two parents, the Cryoshell synthesizes are a new baby matoran.
Stealing away a sacred Nautali, the Rahkshi prepare to complete their plans. Using the Mask of Control as a memory imprint, and the Nuva Symbols as parental energy, the Rahkshi literally rebirth Makuta. Though small and weak, the small Makuta bears all his memories. With time, he can grow into the unstoppable thread he once was, inciting violence across all of Artkahta. The Balrag's dreams will be realized.