More than one hundred thousand years ago, the Great Beings began the creation of the Matoran Universe inside the body of the Great Spirit Mata Nui, in response to the Shattering that struck their home planet of Spherus Magna.
The Great Beings created Tren Krom to watch over the Universe while they gave life to its first inhabitants, the Matoran, and created the Universe's various locations. Artahka and Karzhanni were created, and they constructed their own realms in which they could live. The Hand of Artahka was formed to protect the Matoran. The Great Beings then laid down the foundations of Metru Nui, and created Helryx, the first Toa, to guide the Matoran in the construction of the city. The Kanohi Ignika, created to heal Mata Nui and destroy all life in the universe if things got out of hand, was forged and placed in a heavily guarded chamber, due to its immense power. Eventually, the Hand of Artakha was disbanded, and the Order of Mata Nui, led by Helryx, was formed to serve the will of Mata Nui. The Brotherhood of Makuta was also formed to create Rahi once the Makuta species was created, under the leadership of Makuta Miserix.
The Toa Mata, destined to awaken Mata Nui if anything were to happen to him, were given life and trained in combat by Hydraxon. Once Mata Nui awoke, Tren Krom was imprisoned on an island. Mata Nui appointed the Barraki as rulers of the Universe, and they eventually formed the League of Six Kingdoms. They eventually started planning to overthrow Mata Nui, but were stopped by a Brotherhood of Makuta army led by Makuta Teridax. As punishment for their crimes, they were captured and imprisoned in the Pit. However, their ill-fated rebellion planted in Teridax's mind a plan of overthrowing Mata Nui.
Around seventy-nine thousand, five hundred years ago, Mata Nui began losing his health because a civil war broke out in Metru Nui, causing the Great Disruption. Jovan and his Toa team sought the Ignika, and eventually acquired it, with one member using it to heal Mata Nui at the cost of his life. Following the civil war, Miserix assigned the various Makuta to watch over the regions of the Matoran Universe. He assigned Teridax to Metru Nui for his work in ending the war.
About four thousand years ago, the Kanohi Dragon was released on Metru Nui by the Dark Hunters, as a part of the Shadowed One's plan to take over Metru Nui. Lhikan and the rest of the Toa Mangai arrived to defeat the Rahi, and successfully managed to do so, taking it to Xia afterwards. The eleven Toa then chose to stay in Metru Nui. However, one of their number, Tuyet, was wanted by the Dark Hunters for her possession of the Nui Stone. She began murdering Matoran to make Lhikan and Nidhiki believe the Dark Hunters were responsible, but they learned the truth after defeating them. Tuyet was defeated, and secretly taken to another dimension by Botar. A Tuyet from yet another dimension was placed in the Pit to cover up the Order's plan to reproduce the Nui Stone.
One thousand years after the Kanohi Dragon was released, the Dark Hunters declared war on the city. After discovering Nidhiki had betrayed the Toa, Lhikan set up an ambush with the reinforcements that had arrived, and forced the Dark Hunters out along with the traitorous Nidhiki.
Just five hundred years after the war, Makuta Kojol led a raid on the island of Artakha to steal the Kanohi Avohkii. He succeeded, but Artakha had the Order of Mata Nui destroy everything showing Artakha's location and kill all beings that knew where it was, including Kojol.
Around one thousand three hundred years ago, Makuta Teridax infected Mata Nui with a Virus that gradually weakened him. 299 years after that, Teridax then captured and disguised himself as Turaga Dume, the leader of Metru Nui, and tricked the Matoran of the island-city into spheres that would erase their memories so that when he awakened them, he could be heralded as their leader. He also sent all of the Toa in Metru Nui sent on various 'missions', which resulted in their deaths, until one Toa, Lhikan, remained. He had begun to notice that Dume was acting differently, so he gave Toa Stones to six Matoran, who became the Toa Metru. These six Toa, despite being branded as criminals, were able to expose Teridax and imprison him in a Toa Seal. However, the virus had taken its toll, and Mata Nui was cast into a deep slumber.
As he was traveling between worlds when he fell asleep, Mata Nui began to fall, and crashed into Aqua Magna. This caused massive damage to the Matoran Universe, an event its inhabitants referred to as the Great Cataclysm.
The Dark Time
Due to the Great Cataclysm, a huge part of the Southern Continent broke off and rose to the surface of the planet, becoming the island Voya Nui. A Giant Waterfall was created in Karda Nui, caused by Voya Nui rising to the surface, and water fell into the Southern Continent's dome through the hole that the land had made in the dome and on the Continent. Metru Nui was then invaded by the Visorak horde, led by Roodaka and Sidorak. When the Toa Metru returned to Metru Nui, they were transformed into Toa Hordika. The Toa Hordika, with the help of the Rahaga, managed to scatter the Visorak horde and defeat their leaders. However, Teridax was freed from his prison by a plan of Roodaka's. The Matoran of Metru Nui, still in the Matoran Spheres, were moved to an island on the planet surface of Aqua Magna called Mata Nui, and were awakened by the Toa Metru sacrificed their power to awaken the Matoran, and were transformed into Turaga.
One thousand years later, the Matoran returned to Metru Nui. The real Turaga Dume, who had been imprisoned in a faulty Matoran Sphere and awoken early, informed the Turaga and the Toa Nuva that the Great Spirit was not merely sleeping, but was dying. The Toa Nuva then left on a mission to Voya Nui to acquire the Ignika to save Mata Nui's life. They were defeated, however, by six Skakdi who called themselves Piraka, and were unable to get the Mask of Life. Jaller, a Ta-Matoran, grew suspicious of the Toa Nuva's absence, and after learning from Nokama where they had gone, gathered together five other Matoran to go help them. While traveling to Voya Nui via Toa Canister, the six Matoran were transformed by the Red Star into the Toa Inika. Their Matoran allies freed the Toa Nuva from their imprisonment by the Piraka while they acquired the Kanohi Ignika, only for it to dive into the sea.
The Toa Inika followed the Ignika, and were transformed into the Toa Mahri by it. Following many battles with the Barraki, with help from an unlikely ally in the form of a Maxilos, secretly Makuta Teridax, the Toa destroyed the Cord that anchored Voya Nui to Aqua Magna. Matoro then took the Ignika and followed the sinking island, narrowly slipping below it and arriving in Karda Nui, where he used the mask to revive Mata Nui after teleporting his teammates to Metru Nui, at the cost of his life.
Meanwhile, the Toa Nuva prepared the Matoran Universe for Mata Nui's awakening. After everything on the list had been completed, the Staff of Artakha was used to reverse most of the effects done by the Great Cataclysm. The Toa Nuva were then given Adaptive Armor by Artakha and teleported to Karda Nui to confront the Makuta that had invaded it.
Around the same time, an group of corrupt beings assembled and led by Brutaka traveled across the Matoran Universe on a mission to free the former leader of the Brotherhood, Miserix, and eventually rescued Miserix on an island called Artidax.
The Toa Nuva succeeded in awakening Mata Nui, who rose after his thousand-year slumber. However, Teridax had possessed the body, and exiled Mata Nui's spirit inside the Kanohi Ignika from his body. Teridax, exercising his new powers, then made an announcement to the entire Matoran Universe of his victory. The Matoran of Metru Nui were enslaved by the new "Turaga," Ahkmou, while other disparate groups joined together in small resistance groups to rebel against and reclaim the Matoran Universe.
Eventually, Teridax landed on Bara Magna, with the intent on destroying Mata Nui. He released many Rahkshi of Heat Vision from hatches in the Matoran Universe onto the planet. Takanuva migrated onto Bara Magna as well, followed by Tahu.
During Teridax's fight with Mata Nui, Mata Nui pushed Teridax into the path of a fragment of Aqua Magna. The resulting impact destroyed the Core Processor, killing Teridax and heavily damaging Metru Nui. With no being in control, the robot body collapsed onto Bara Magna, causing damage throughout the Matoran Universe, as well as causing the heating, lighting, and artificial gravity systems in the robot to fail. As a result, most beings in the Matoran Universe migrated to the newly reformed Spherus Magna.
Great Spirit Makuta Alternate Universe
In this reality, the Great Beings named the Matoran Universe's guiding spirit Makuta, and his brother Mata Nui plotted against him.
In this alternate reality, Tuyet formed a Toa Empire, conquering some of the Matoran Universe, and ruling it as an empress.
In this alternate universe, Matoro failed to revive Mata Nui, and as such a mass exodus of the Matoran Universe happened, with all but the Zyglak and Makuta exiting the universe. Pit Mutagen leaked into the universe, and in three days the heat, light, and gravity systems failed and surviving Rahi were mutated. The Zyglak died, and Teridax took over Icarax's and merged with the bodies of each Makuta when they died. Teridax created Rahkshi coated in thick shadow armor to survive passing through light barriers placed blocking the way to the island of Mata Nui above.
The Matoran Universe inhabitants left it when Mata Nui reformed Spherus Magna in this universe.
The Matoran Universe is comprised of a variety of domes; massive individual caves separated by gates with oceans and islands of their own:
▪ The island city of Metru Nui is contained within the most prominent portion of the domes. The city does not share its dome with any other islands. It acts as the Great Spirit's brain.
▪ Karzahni is contained within its own cavern, and is connected to the Metru Nui dome by a series of mountain ranges, a large stone gateway, and a short isthmus jutting into the Metru Nui dome. This isthmus was used by the future Toa Inika on their way to Voya Nui.
▪ Artakha is situated to the west of the Northern Continent.
▪ The Southern Continent is situated south of Metru Nui and is far larger than Mata Nui. There is a series of underground caverns underneath the continent, which was home to the Av-Matoran. These caverns are situated on top of the stalactites in Karda Nui.
▪ Voya Nui was originally connected to the Southern Continent, located south of the Metru Nui and Karzahni domes. During the Great Cataclysm, it was violently torn from the continent and thrust upward through the roof of its dome. It floated upon the Endless Ocean, south of the island of Mata Nui, and moved little from the point it emerged from since that time. It was later returned to its former location when the Toa Mahri destroyed the Cord.
▪ Karda Nui is located beneath the Southern Continent, and is considered to be a world of its own. It acts as the Great Spirit's heart.
▪ There are two chains of islands situated far in the south of the Matoran Universe which includes chain of active volcanoes that were capped by the Toa Nuva. They remain mostly unexplored, and have little known use.
Description from : http://biosector01.com/wiki/index.php/Matoran_Universe