The movie never explains this, but the elemental powers of the Toa got depleted during their off-screen ventures (detailed in the books and comics), of which we only see a short montage in the movie. By the end of the film, their powers have recharged, which is why they only use them then.
Makuta intended to enslave the entire Matoran population of Metru Nui into capsules. These had the effect of, over time, erasing their captives' memories and deteriorating their bodies. Makuta wanted the Mask of Time to be made as it would have allowed him to speed up the time around the capsules, thereby having to wait less for them to take effect, so that he could awaken the Matoran and fool them into thinking that he was their savior.
The six Toa use their elemental powers to form a crystalline cage of solid protodermis (the substance that the BIONICLE world is made of) around him. In the BIONICLE world, the combination of any six elements that don't cancel each other out can create protodermis.
Nidhiki was once a Toa hero and served together with Toa Lhikan, developing a brotherly relationship with him. However Nidhiki grew power-hungry and ended up betraying his Toa fellows and joining the mercenary organization of the Dark Hunters. He was subsequently mutated by Roodaka (the villain in Bionicle 3: Web of Shadows (2005)) into the insect-like form we see in the movie, to ensure that he would never return to being a Toa hero again.
The Mask of Time doesn't allow time-travel. It can only slow down or speed up time around a given target, but its user cannot travel back in time with it.
Yes. His right eye got poked out by a female Makuta named Gorast long before the events of this movie.
The Brotherhood of Makuta, the evil organization that he's the leader of. This was one of the first hints in the BIONICLE storyline that there was more than one Makuta.
The Morbuzakh plant, which had a great presence in the comics, novels and games leading up to the movie's story, only has a short cameo, during the Toa Metru's "scavenger hunt" montage when its vines are seen holding Vakama prisoner.
The act itself isn't shown nor explained, as it happened many years before this movie. He had released a virus that over time shut Mata Nui down, and waited until it had taken effect (which happens during the movie) to reveal his evil intentions to the world.
The Makuta were originally good and served to protect the Matoran, as well as to preserve nature's balance by bioengineering wild life. They had crushed conflicts several times before turning corrupt, but had kept their intentions secret. That's why everyone is surprised to see that Makuta is behind the Matoran's disappearance.
The play-field the Toa have to go through is called the "sea of protodermis", later we find out that the actual sea surrounding the island is made of liquid protodermis, and at the end the Toa trap the villain inside crystalline protodermis.
Protodermis is a (probably artificial) substance that everything in the Matoran Universe is made out of, so it's basically synonymous with "matter" for the characters. It can be liquid, metal, wood, crystal or even flesh; not that the movies ever explain what it is. However the waters in the previous movie were made of actual water, since it took place on an island outside of the Matoran Universe.
Protodermis is a (probably artificial) substance that everything in the Matoran Universe is made out of, so it's basically synonymous with "matter" for the characters. It can be liquid, metal, wood, crystal or even flesh; not that the movies ever explain what it is. However the waters in the previous movie were made of actual water, since it took place on an island outside of the Matoran Universe.
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