you just have to play the game
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You have see to many different pokemons. Then you will fill it (you have to every Pokemon to get national pokedex).
fill your pokedex and battle more trainers
you have to win the champion and fill your pokedex. (^^)
Do you have Giratina? Do you have a national pokedex? did you get Heatrans? If you have a national pokedex you can go to Celestic Town and go in the cave and observe the inscription. Cynthia says that it may not be the three lake Pokemon. maybe it's Dialga, Palkia, and Giratina. I dunno. I'm kinda at a loss, too... Just try to fill up your pokedex, i guess...
A Gengar can be seen in a battle with Psychic Bryce in Victory Road.