I made an old theory on this but I think diferently now. I think paradise (the one referred to in the beggining of time movies) is more like a parrallel plane to mata nui. Evil would be imprisoned in kini nui, in the same sunctum mata nui is in. The bohrok were originaly the holy guards that served in the war against pure evil. Then evil escaped from its prison, and posessed makuta. The bahrag who were guarding evil's prison turned their armies of Bohrok against the mata nuians, through a portal. They were assined to guard the matanuians by the great god, who is buried in ta koro. Mata nui created the toa to help with this task. The were made to quench rebelion. So watcha think, any questions, thoughts, comments, flaws to fix, things to flesh out, etc., etc., etc.
EDIT: whoops this is already there. Could someone close it?