You will find him on the Plasma Frigate.You need to beat everyone in the Frigate and you need to know also a password which is: 1101 2202 3303 4404 5505 6606 7707 8808 9909 Remember that is only one of them so try all. It is different in every game.
On the plasma frigate if you beat someone he will add them to your pokedex(this is after you have all gym badges) Btw he also adds Zecrom
