Ending Zero in Garden Society Kykuit. It has been accessed post-release, but nobody quite knows how to do it - retracing the posted steps doesn't always work.
The Mata Nui Online Game's first released "chunk" ended with you clicking on a shadowy figure who appears near the beach, triggering a short cutscene of him turning to look at you. When LEGO re-released the game for download, this bit was dropped as it would have caused continuity issues if you played the game in one sitting. However, the cutscene is available to watch in the animation collection, and the later re-release on Templar Studio's site still has it in the game.
One unused game file shows a villager creating a Comet ball. According to one of the proposed ideas, the bazaar trader who sold these balls would have held a group of villagers prisoner to make these balls for him. Another scrapped idea involved a seventh mystery tribe existing on the island and working for Makuta. This would probably have been another mystery for the player to solve.
Throughout the game, characters give you advice for fighting Kofo-Jaga scorpions, even though none ever show up. Another absent creature that gets mentioned in the dialogue is the Sand Tarakava, a figure LEGO intended for release but canceled during the game's production.
Parts of the backstory got dummied out too. Originally, the characters would have mentioned beings of great importance called Papu and Rangi. To avoid any more controversy from Polynesian people for borrowing concepts from their culture, these names were removed, but two speech files still have them: after you show Nuju's letter to Nokama and ask "Who am I?", she says "Papu and Rangi have plans for you" instead of her normal "someone has plans for you". And in the German version, Jala refers to them as the founders of Ta-Koro, a bit that doesn't come up in the original English release.
There was to be a side-quest where you join a search party looking for Onua. Aside from an unused game file in which a so-called commander asks if you want to join, no other trace of this plot-line remains.
The interior of one of the Onu-Koro huts has also been cut, but the scene's prototype can be viewed in the game files. Apparently, the hut belonged to a "Biodermis smith" ("biodermis" being an early name for protodermis), a character who doesn't show up in the released version.
The German version of Jala's conversation was translated from a different text file than what's used in the English release, and contain info that's not found elsewhere. Apart from the odd mentions of Papu and Rangi, German Jala introduces himself as a member of the tribe of "Lhii Surfers" and a participant in the "Great Haka Dance". The latter is an actual Maori dance that never comes up in the Bionicle lore, while Lhii was later explained in the story as being a legendary lava surfer — the legend serves as a memory of a character called Lhikan whose mask was given to Jala.