Through a gigantic Xanatos Gambit involving dozens of people and backup plans as well as thousands of years, Makuta has effectively become the new god of the matoran universe, dethroning his Brother Mata Nui, and sealing his soul into the Mask of Life(As both were made by the Great Beings, the Protheans of the bionicle universe, makuta would not dare destroy them).
It was revealed that the matoran universe is actually a planet sized andriod, the true form of Mata Nui.
He was created to explore the universe, and as far as we know, find planets for colonization by the great beings, since their own planet, Spherus magna, is literally breaking apart at the seams due to centuries of warfare over Protodermis(plhebonium).
the online stories one can read at bioniclestory.com detail many of the adventures had by the bionicle gang between the time of the 3rd movie and this one, adding the series of Bionicle Legends books from scholastic, the story can be read in its entirety.
This brings us to bara Magna, the planet which mata nui(trapped in the mask of life, which is on the cover) has landed on which has its own share of heroes and villains already in the midst of a war.
Now Mata Nui has to create a new body for himself, gather an army, and build/get a spacecraft/fleet large and powerful enough to reclaim his throne and destroy his brother makuta.
However, the matoran, after learning the purpose of their entire lives, culture, and races is essentially "nanotech management" of Mata-Nui's functionality, may not want to exactly go back to how things were.