This storyline in the Bionicle timeline takes place long before the 2001 one.

In Metru Nui, it's a big metropolis, ruled by Turaga Dume. There were other major events here, but they aren't important yet.

A plant creature called the Morbuzahk wrecks the city. Toa Lhikan gets 6 Toa stones from Ga-Metru and gives them to 6 Matoran to get them into Toa. At the last one, after he gives one to Vakama, he gets captured by Nidihki and Krehka.

All Matoran with the stones go the Ga-Metru to turn into Toa. They all have their differences from where they came from, so they have some problems. They plan their first mission is to find the Matoran that know where the Great Disks are and use it against the Morbuzahk to rid of it forever. They manage to get the disks from each Metru and go into the Great Furnace to vanquish the plant.

Going to the Collesium, they show the population that they're Toa, but then Turaga Dume decides a test to prove it. Unfortunately, they fail and are accused of being crimminals, and now have Vahki hunting them. Whenua, Owena, and Nuju are caught, while Vakama, Nokama, and Matau are on the run. They manage to find each other at the Dark Hunter prison in underground Po-Metru, and find out that Lhikan has become a Turaga and that the real Turaga Dume was done here too, meaning the Dume at the Collesium was acutally an imposter. When the group gets back to the Collesium, they found out the imposter was Makuta, who already ordered all Matoran into capsules and go inactive. In a Vahki transport, the group takes a few capsules (which are very big) in it and attempt to get to another place through a crack (meanwhile, Vakama makes the Vahi he promised the imposter Dume). Makuta attempts to intervene, but their combined efforts, they got through the obstactles. When Vakama goes to confront Makuta, Lhikan dies protecting him, the Mask of Time falls into the ocean and Makuta is imprisoned in protodermis by the Toa.

The Toa managed to get to an island which they call Mata Nui. With only a small fraction of capsules (minus one that was lost on the way). They start to go back to Metru Nui to retrieve the rest of them.