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Unknown until Micro$oft takes over and possibly destroys the Halo franchise. Elites have turned against the Covenant, and the Prophets encountered in the games so far are dead, but all of the others are the same-old Covenant we've been blasting for years.

It is possible that the species that were loyal to the elites (Hunters and the Grunts that spoke up to join the Elites, in halo 2 cortana says they are to scared to speak up but some did ) went to their home planets, or they went to Sangheil with the Elites, or they could have stayed on Earth, other than those theories it is unknown what happened, yet with the possible upcoming of Halo 4 it may be revealed then.

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