You get the Rainbow Pass by giving Celio the Ruby gem, which is located on island 1 at the bottom part of Mt. Ember, where 2 Rockets are near a hole in a wall. Enter there, and you'll have to do a sort of puzzle, then obtain the Ruby gem. Go back to 1 Island, give Celio the Rub, and he'll ask you to do a favor. Say yes, he'll give you Rainbow Pass and ask you to get the Saphire. You go ot Island 4, go to the right of the screen, surf towards the cave, then navigate through it and you'll get the Waterfall TM. After that, go near the entrance of the cave, and use waterfall up it. You'll go through some stairs, and then see Lorelei battling Rockets, and you join in.
Edit, remember after you beat Cinnibar's gym how bill got you on a boat and took you to One Island? The guy Bill was talking to was Celio, in 1 Island's Pokecenter. Go to Vermillion, to the SS Anne port, and get to 1 island