espeonrules

Best answer as chosen by Asker / Ratings
First, you will need to go back to Mossdeep City, so fly there. Be sure to bring along Pokemon that know Surf, Dive, Strenth, and Rock Smash. Okay, after making sure of that, surf south of Mossdeep and use Dive on the long dark patch of water that you see. Follow this path and go south until you see a cave enterance. Go in and press B to surface. Go onto to land and into the cave. You should now be in Seafloor Cavern.



Now head north, solving the HM puzzles on your way, and go into the door leading to the next room. Next, go through to the top left enterance. You should be in a room with currents. Use Surf and manuever your way to the top left enterance again. Solve the puzzle in the next room, then go to the room after that. Save here, because you will be facing Archie here. Follow the path to him and beat him. Archie will then use the Red Orb on Kyogre, who then flees. You will be taken outside, where the weather is raining, combined with solar flashes. Steven comes, and tells you he will be going to Sootopolis City. Now, Fly over there.



Once you arrive, you'll see a little cutscene with Kyogre and Groudon fighting each other. Go around them, and you'll see Steven, Archie, and Maxie. Talk to them, and Steven leads you to a cave. This is known as the Cave of Origin. Head through the cave, and then you'll see Wallace, the former Gym Leader here. He will ask you where Rayquaza is. Choose Sky Pillar. Now, you should head there. To get there, surf onto Route 131. Use the Pokenav to help you get there. Surf along the north side of the route, until you see a little gap. Go through this gap, and you'll see Sky Pillar.



Head inside, and you'll see Wallace again. After some eartquakes he'll leave, leaving you to go all the way to the top via the stairs. Once there, you'll see Rayquaza, who'll immediatly fly off to Sootopolis. You can go to Sootopolis now, or surf west to Pacifilog Town, if you haven't been to this town already. Otherwise, fly to Sootopolis, where you'll see a cool and neat animation with Kyogre, Groudon, and Rayquaza. After that, the crazy weather will stop and all three of them will go away, returning Hoenn to it's peaceful state once more. Now, surf to the Gym where you'll see Wallace, Steven, Archie and Maxie. Talk to all of them, and Wallace will give you HM 07-Waterfall. Now you should be able to go into the Gym to fight Juan-good luck, and hope I helped!


~espeonrules