- The game is available in three versions, none completed or ever released officially:
- The alpha build (dated July 2001) is less complete and functional by far, but contains elements inspired by real-life Polynesian cultures, like the Haka, a type of ritualistic dance. It also features more cutscenes, such as Onua meeting Nobua and exploring Onu-Koro. The exposition relayed by the Turaga details the Legend of the Bionicle. Enemy creatures are very sparse, and a number of villagers (some of them named) are found in all villages, and in Onu-Koro, many of them are dancing. This version of the game contains stones with gameplay hints, players can upgrade their abilities, most defeated enemies revert back to harmless animals, and at the end the Toa Kaita would have been playable as they fight the Manas crab monsters.
- The beta build (from October 2001) is the farthest the game ever got in its official development phase. All levels were redesigned, most notably Ga-Wahi, which looks completely different. In-engine cutscenes, the character Nobua and Haka dances were deleted, tutorial stones removed, and the dialogue greatly simplified, with the Turaga providing no backstory. There are many creatures roaming the environments, which disappear upon their defeat. In some villages, the people only come out of hiding after the animals have been dealt with. The Kaita and Manas stages were cut, replaced instead by a pre-rendered cutscene.
- Neither version features the Toa's climactic confrontation with the Shadow Toa, nor their clash with the main villain Makuta. Despite being talked about, Makuta was not meant to appear in the game, as he is also absent in the 2003 novelization of the story, Tale of the Toa by Cathy A. Hapka. Alternate takes on the "Toa Kaita vs. Manas" and "Toa vs. Makuta" fights have been told in the Mata Nui Online Game (2001), which was released instead of this game.
- The "Rebuilt" version is a fan-made combination of the alpha and the beta builds, created by the Litestone development team. This work-in-progress version attempts to fix the game's glitches and make it as complete as possible. They have reinstalled the content cut from the alpha, added characters from other parts of the Bionicle franchise who were not originally in the game, and inserted nods or in-jokes that only fans will understand. They are also planning to add content not found in either official build for better gaming experience, mainly the aforementioned final boss fight against Makuta.
- At least two versions of the intro sequence exist. The more famous one, released via Lego's promotional material in 2001, featured an organic, reptilian "bird" finding Onua's canister and pecking at it before it opens. The finalized version, first revealed through gameplay footage posted to YouTube in 2010, replaced this creature with a robotic bird made out of actual Lego Technic pieces.
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