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Actually, what you have to do is first recruit Dialga and Palkia, then do three random missions and you should recruit Manaphy. After that do another 3 missions and Manaphy will tell you about a dungeon, then just quick go through it and your able to evolve.
My sister would probably screw up, and you don't get it. Just about everyone where I live hates pokemon. People who like it are the ones who get picked on. I'll just say I'm doing it for my sister since shes sick though.