This game is the only media to depict the Toa's first confrontation with the evil Makuta. Nor the comics, nor the scrapped PC game Bionicle: The Legend of Mata Nui (2001), nor the first Bionicle novel features this scene. It was created solely by the developers of this game after Lego had given them the freedom to write the ending to the story, since the game Bionicle: The Legend of Mata Nui (2001) had been canceled.
In the Charred Forest, if you watch Kapura for long enough, he will produce fiery clouds of flatulence that propel him forward.
During the Le-Koro celebration, the two Matoran dancing on the right do the robot if you observe them for long enough.
The game was designed with many more story-lines and mini-games in mind. Although a lot of these were dropped, there still exist references to them in the finished product. For example, many characters give you advice on how to fight Kofo-Jaga scorpions, and later even Sand Tarakava, two creatures that do not appear in the game at any point. Some unused game-files also reveal canceled content: like a search party looking for Onua, and also a mystery relating to a secret, evil seventh tribe.
The masks of two otherwise near-identical looking characters, Hafu and Taipu, infamously got mixed up. This was given a humorous reference in Mata Nui Online Game II: The Final Chronicle (2003), where they are drawn with their correct masks and Taipu angrily mentions that people always confuse them.