Below is a list of alternate universes seen in the story.
In one alternate timeline, Lhikan was killed by Nidhiki during the fight with Tuyet. This resulted in Tuyet taking over the universe and establishing a tyrannical Toa Empire.
Metru Nui was intact and beautiful. Unlike the main universe, Metru Nui had statues of Toa everywhere. There were statues of the Toa Mata in their original forms, as well as statues of Toa unfamiliar to Takanuva. Looming over them all was a massive sculpture of the Mask of Intangibility. Toa were required to carry an identity tablet; to not carry one was considered an act of war against the Toa Empire.
Vahki served the Toa and guarded the Coliseum, where prisoners were kept. The Matoran Takua was imprisoned here after he spent more time wandering than working and punishment by the Vahki did not take. Gali resided in Ga-Metru, where she ran the re-education center with Karzahni.
About 3,500 years before story year 2008, Toa Tuyet tapped into the power of the Nui Stone, which gave her the power of maybe 100 Toa. Toa Lhikan tried to stop her and was killed by her and his traitorous friend, Toa Nidhiki. Tuyet took over Metru Nui and convinced the other Toa that it was their destiny to smash anyone who posed a threat to the Great Spirit, including everyone from the Makuta to the Dark Hunters, to Toa who were not enthusiastic enough or Matoran who did not work quite hard enough.
In this universe, the Archives served as a museum of conquest. Here Takanuva saw a long-dead Visorak mounted on display. He also saw a collection of weaponry, each item labeled with a tablet. Included were the staff of the Shadowed One, the Spear of Fusion, zamor sphere launchers, Rhotuka launchers, and more. Most impressive was the Mask of Shadows formerly worn by Teridax, nailed to the wall like a trophy. Deeper in the Archives was a group of stasis tubes. In one of these tubes was kept Turaga Dume.
When Tuyet took over, Turaga Dume spoke out against her and said that true Toa valued justice and mercy, and she had none. Turaga Dume was hauled away and trapped in a stasis tube kept on display in the Archives.
In this universe, Toa Tuyet was the leader of the Toa Empire, the wielder of the Nui Stone, and the unquestioned ruler of the known universe.
Tuyet kept the Mask of Shadows in the Archives unguarded as a taunt to Teridax, knowing that he longer for it but could not touch it. It was rigged so that if it were so much as touched, Tuyet and her minions would know immediately.
In this world, Makuta were hunted fugitives. Teridax, Krika, and Kojol hid in the depths of the Archives. They needed to shapeshift when venturing outside. Deprived of his Mask of Shadows, Teridax instead wore a scarred and pitted Kanohi Hau.
Weeks before Takanuva's arrival, a Matoran expedition escorted by two Toa was sent to Artakha to retrieve the Mask of Time, one of the few weapons that might be effective against Tuyet. The Matoran leader of this expedition was Jaller [sic], a fanatic servant of the Empire who was willing to die for its cause. The Toa escorts were Bomonga and Kualus.
Kodan kept a record of every Toa in the universe.
In this universe, Bomonga had killed Brutaka. Brutaka tried to prevent the Toa Empire's exploration of Voya Nui, making him an enemy of the Empire. Brutaka fought well, but when he turned to fight Gaaki and Pouks, Bomonga hit him from behind, finishing him off. Brutaka's weapons and mask were taken to the Coliseum, where other treasures were kept for safekeeping.
Kualus remarked cynically that it was difficult having a conscience in the Toa Empire. From his point of view, keeping the Matoran in fear of the Toa was an effective way to make the Matoran respect the Toa as well.
A group of Toa including Bomonga, Kualus, and Naho was sent to Odina to clear out the Dark Hunters. Naho offered to go after the Shadowed One by herself; she secretly intended to help the Shadowed One escape, presumably because she disagreed with the Toa Empire's ruthlessness. Although the Shadowed One got away, Naho was discovered and captured by the Toa. Tuyet turned Naho over to Roodaka, who mutated her. Naho ended up as an exhibit in the Archives.
Tuyet was friends with Roodaka.
Lesovikk was the most wanted enemy of the Toa Empire. Lesovikk desired peace and believed it to be impossible with Tuyet in power. Because of this, Lesovikk kept an eye out for things Tuyet wanted and stole them first.
The Throne of Stone was a huge throne in Po-Metru where Pohatu sat. It was located in the Po-Metru Sculpture Fields. It was a huge throne made of rock mounted atop a base of Rahkshi parts. Po-Matoran bearing torches surrounded it. At a certain time of evening, the Po-Matoran left to return to their homes, and Pohatu descended from the throne. Lesovikk would scrape his foot against a rock three times to send a secret signal to Pohatu to meet.
Items such as Brutaka's mask were kept in the Hall of Masks in the Coliseum.
Tahu, Pohatu, etc. were supposed to remain asleep until they were needed to awaken Mata Nui. Mata Nui never fell asleep in this universe. Tuyet found out where the Toa Mata were from Artakha. She sent some Toa in to find them, but none of them survived the trip. That was when Tuyet discovered a spot in the Coliseum that no one had ever seen before: a place from which she could fake the signal that would launch the Toa Mata's canisters. This is how she awakened and released the Toa Mata. When the Toa Mata were awakened, Tuyet laid out how the Makuta and Dark Hunters were plotting a takeover, and it was their duty as Toa to stop them dead, as it was the only way to make the universe really safe. All of the Toa Mata signed on, but after a while, Pohatu started to have doubts. These turned to fears when Pohatu discovered that Tuyet had sent a squad of Toa led by Toa Nidhiki to wipe out the Nynrah Ghosts, just because they had the potential to make something that might someday be used against Tuyet. This resulted in the deaths of four dozen Matoran, which sickened Pohatu. Pohatu made contact with Lesovikk, and the two secretly worked against Tuyet ever since.
Pohatu had his own cavern in Po-Metru. He could signal members of his resistance group by sending a mild tremor the length of Metru Nui, which would instruct them to come to the cavern through underground tunnels. The members of this group were Nuju; Ahkmou; the three Dark Hunters Guardian, Darkness, and Primal; one Toa, Krakua; and the Po-Matoran Kodan, who was also the Chronicler of the Toa. It was useful to have the Toa's Chronicler on their side, as it kept them informed.
Pohatu had a protosteel axe to wield.
Tuyet believed that she had given the Matoran peace. In her mind, by ruthlessly stifling enemies and terrorizing villagers, she was just doing what had to be done to keep that peace.
Brutaka once opened a portal to what he claimed was a dimension full of beings made of solid light. These beings fed on shadow and would have made a food bank of a Makuta.
Close to 100 different alternate universes which Makuta Tridax visited using a Kanohi Olmak. He kidnapped each universe's version of Takanuva in order to build an army of shadow Toa. See Takanuva Army.
Mazeka and Vultraz arrived in this alternate universe after going through a portal in Karda Niu. They found themselves in some woods on Spherus Magna and saw a massive tree banded with golden metal. There was also something that looked like a lake, but whose waters undulated like some vast organism. When Vultraz's skyfighter flew by it, shards of razor-sharp crystal flew from the depths of the pseudo-lake, slicing pieces off the vehicle. The instant the vehicle made contact with the surface of the creature, it transformed into sheer energy and disappeared.
In this universe, Macku had the appearance of a Ga-Matoran, but had the powers and title of a Toa. Anyone who looked like a Matoran was considered a "hero of the Melding." Helryx, whom Macku described as an "oversized mass of muscle," was one of Macku's villagers and had the appearance of a Toa of Water. Helryx was a tall, blue-armored figure. Macku and Helryx had never heard of Mata Nui. Spherus Magna referred to the whole planet they were on.
In this universe, the Great Beings created Toa to be agile, fast, and small, intending for them to take on the tough jobs. The Matoran, who were larger, were supposed to do the work the village needed done in order to thrive. As a Matoran, Helryx was disappointed that she could not have helped save Spherus Magna like the Toa did. Takua was known for telling the story of the Melding well. Kapura was also a Toa.
A little over 100,000 years ago, some villagers discovered a silvery liquid (energized protodermis) leaking out of a fissure and went to see what it was. They touched it, and in an instant, they were destroyed. Later on, someone else tried to scoop a little up, and their tool turned into a trident. Because the substance was so powerful, everyone started fighting over it, never paying attention to the fact that it was spreading all over. The Great Beings saw what was happening, and they knew if it did not stop, the planet would be shattered into pieces. The Great Beings rejected their first few ideas for a solution. Finally, they created a handful of powerful beings called Toa, with elemental powers and mask powers. The Toa went underground to retrieve the liquid in special containers and try to fix the damage. This was hard work, with plenty of cave-ins, but the Toa's small size made it easier. Over the better part of five years, the Toa managed to meld the planet back together.
Macku and Helryx were from a village located in a clearing in the woods. The village was filled with large Matoran like Helryx, but there were no other Toa like Macku.
Gali ran a canoe business. Macku heard she had been as far south as the mountains, but not much past that. Macku did not think there was much beyond the peaks worth seeing. [Perhaps this was referring to the Bara Magna desert.]
The Great Beings knew Spherus Magna better than anyone, from the Great Sea to the Northern Frost.
In this universe, Makuta Teridax was a tall, white-armored being. The role of the Makuta in this universe was to aid the Toa in looking after the villagers, to create new life forms as needed, and to teach the virtues of unity, duty, and destiny to those they brought into being. Vultraz wondered if the Makuta turned out differently in this universe because the Makuta's actions in his own universe were driven by hatred for and jealousy of Mata Nui, and Mata Nui did not exist here. In this universe, a Makuta had to be a being utterly without doubt, fear, or any trace of shadow. It took long years of meditation before one was ready to assume the title. The powers that once ran the world [the Element Lords?] were mad with a hunger for power, so the Great Beings created the Makuta as an answer to that.
To get from the forest where Mazeka and Vultraz arrived to the Great Beings' fortress, they had to take a long and dangerous trip through thick forest and high mountains. Now and then, a great roar would shake the earth; Teridax did not offer to explain what this was. The Great Beings' fortress they visited was a vast fortress made completely of crystal and iron. Two white-armored Makuta, Gorast and Icarax, guarded the main gate. When Vultraz commented on Gorast's appearance, she slammed on the ground telekinetically as a warning. The "telekinesis" Gorast used on Vultraz was actually a use of her gravity powers. The journey from the main gate to the central chamber took even longer than the journey to the fortress. It had so many twists and turns that Mazeka was convinced it was meant to make it impossible for visitors to remember how to find the Great Beings.
The room where Teridax brought Mazeka and Vultraz to meet the Great Beings looked like a council chamber. A semi-circular stone dais sat at the far end of the room. The only illumination came from lightstones embedded high in the ceiling, and that was barely enough to see one's hand in from of one's face. For a moment, Mazeka thought he could dimly make out six figures seated at the dais. When the first Great Being spoke, the voice was soft, no more than a whisper. Another whispered voice sounded strikingly ancient. The Great Beings continued to speak in whispers.
The Great Beings said they had many wondrous creations, some even "loyal Teridax" did not know about. The Great Beings were aware that they had counterparts elsewhere in the vast, uncounted realities that existed. Because of this, Mazeka and Vultraz's appearance was fascinating, but not a surprise to them. They thought that it was only a matter of time before one of their creations pierced the dimensional walls.
Chirox and Vamprah appeared in the Great Beings' chamber to take Vultraz away.
In this reality, Mata Nui had never been needed to be built in the first place.
In one alternate timeline, Lhikan and his original team were saved from the frostelus by a squad of Toa led by Toa Lesovikk.