I got it, and I'm still working at it.
The actual game is pretty long and that Deoxys mission is available after you reach a certain point in the game-you'll know when you reach it. But there is a point where you NEED more than one player to get through a certain part of the game (Doesn't affect the Single Player game). I'm at that point now and its TRULY aggravating.
I loved this installment as well, still fresh and awesome. The game is crazy and the story is nuts, completely nuts.