The Brotherhood of Makuta\Dark Hunter War was a conflict between the Brotherhood of Makuta and the Dark Hunters, indirectly instigated by the Toa Metru. It started in the Great Temple in Ga-Metru when the Shadowed One noticed that Makuta had killed two of his Dark Hunters, Nidhiki and Krekka. The Shadowed One used his laser eyes to break off Makuta's wings. Makuta threw him to an unconscious Voporak.
Very little is known about this conflict. It is known that Roodaka served as a double agent for both factions.
The Brotherhood are having problems with this, simply because they know that they can easily destroy the hunters, but Toa are hurting both sides, so each side has two enemies.