Beat the champion, after that you beat the game, after you beat the game one or more rare legendary pokemon usually become availailable in caves. Should check out if there's any ships going to places not accessible before In red , blue and yellow, go to cerulean city and find the cave where mewtwo is. In gold, silver (edit) In crystal (edit) In ruby , sapphire (edit) (battle tower?) In emerald you can go to the battle frontier ( i tought it was by boat ) (incomplete)