How do I make a Pokemon MMORPG?
You program it. Not much more you can say than that. If you know PHP and MySQL, then it should be a fairly trivial task. The hard part is planning it, and the amount of time it will take for one person to do all the work. The only way I could tell you more would be to do it or start doing it for you, and then that’s not telling you how to do it, that’s me doing it for you. If you really have no clue, get some more practice with the languages, and have a look at simple games made in PHP to see how to make the interactivity.