Pokemon XD Gale of Darkness question....?

okay, so i finally caught the remainder of Master Greevils pokemon ALL OF THEM. I go back to citidark isle and i go up to master greevil's place again, and he battles me again with other pokemon! I thought he agreed that cipher was done for! And wasn't I supposed to find Miror B. at Gateon port after I defeated Greevil then capture dragonite? Please help. Why haven't I defeated cipher, i caught all of his shadow pokemon including lugia!