Now that you can use HM08 outside of battle, look at your Map on your Pokemon Navigator. Locate an island Southwest of where you are, and surf there. Go to it from the south, and look at the first image below. When you are there, or anywhere on that 'darkened' water, use the Dive attack. You should be underwater, and you should see the second image. If not, dive around for a bit until you find the opening. Then go in, and 'undive' by pressing one of the buttons. You should rise up again, and into Sootopolis City! This place is divided by water down the middle, with the Pokemon Center to the right, Pokeshop to the left, and the Gym right in the middle. The Gym is currently closed sadly, so you cannot enter yet. Just look around, and talk to some people. Then when you are ready to leave, fly back to Mossdeep City, and surf all the way south. Then head west to KiWinona Town. There isn't much there, but talk to everyone anyway. Now we have gone to all the towns but one, so this should make Flying around easier. Now Fly back to Takusane City, and surf south. You should see some more dark water, and so dive under. Continue down as south as you can, only changing direction if you cannot go anymore south. Just continue along until you reach a cave enterance, shown in the 3rd picture. The 4th picture shows what you see above the water level.
Now enter the cave. You will see a submarine! Team Aqua is here, so get ready for some
fighting. Float up from the submarine, and just head north. You will enter Kaitei Cave. This place also has some easy puzzles, but can be annoying. Be sure to have someone with Strength and Rock Smash! Head north from the first room. You will find yourself in an large room with many boulders. Don't worry about them now, and head to to room to the left of it. Once you go down there, head back up to bring the boulders back in place. Hit the first boulder north, then head west. Head east and push that boulder to the right. Then hit the boulder that is north of you, north. Then smash that rock, and go some more right. Push that boulder that way, then go north into cave. You will find some quick moving water, so you have to do this carefully. Surf on the water, and head to the south part moving east, then go east some more onto the next current. You will stop between a few currents, then go north. Once you get off that current, go north. Then when your done with that one, go to the wall and then north again, and your free. This part is easy, so push them aside and go fight the trainer. This next room is difficult. You will see three boulders near you. Push the first and third ones north, then the middle one either east or west. Then push the boulder in the middle north once. Push the one to the left, in the left direction, and the one to the right, to the right direction. You will see 3 pushable boulders ahead of you. Push the first and third one north, then move the middle one either left or right, then you are clear. This place is foggy, but you will eventually find some aqua members, with Kyogre in the water/Groudon in the lava. The Aqua/Magma leader will let out a light to make the legendary leave, then Team Magma/Aqua will come. You will all go outside, and see terrible rain and thunder, or massive heat if you have Ruby. Now fly back to Sootopolis City for some more cave fun.
Once back at Sootopolis City, head for the eastern part of the City. Head north and you will run into a few people. The will talk to you and stuff, and then go to Cave of Origin. You will need a Pokemon with Flash. Once inside, you will find that this is a fairly simple path. You will eventually find HM07 here. You will feal and hear rumbing, ignore them and continue on. You will eventually find Kyogre, and it will fight you! It will be level 45, and know Body Slam, Ice Beam, Hydro Pump, and Calm Mind, which increases its Sp. Attack and Sp. Defence. If you are fighting Groudon, it will have Slash, Earthquake, Fire Blast, and Bulk Up. Bulk Up can make it increase its Attack and Defence, so watch out. It is not that hard to weaken, however its characteristic makes it rain/sun like a it used a Rain Dance/Sunny day, making its water/fire attacks more deadly. Also, if Kyogre or Groudon make the rain/sun in this way, it will not vanish, even after 5 turns. Once you catch or beat it, go outside, and everything should be normal. Now head south to the gym! Its the water gym, and is not as hard as some of the others, but it can be tricky. There is a puzzle here, and if you fail it, you fall down and fight a few trainers. I recommend falling at first so you can fight them all. The answers to these puzzles is shown below. You must step on each square once, and your last square must be at the exit. Once you finish the 3 trials you will find the gym leader. Wallace, the gym leader, has 5 Pokemon. His first Pokemon is Luvdisc, who is level 40. He is not to hard to beat, and will give out 942 Exp. His second Pokemon, Whiscash, is much harder. He is level 42, and he is a Water/Ground Pokemon. I recommend using a Grass type instead of an electric here. It will give out 1422 Exp. His third Pokemon is a level 40 Sealeo, a Water/Ice Pokemon. Sealeo will give out 1096 Exp. His fourth Pokemon is a Seaking, is level 42, and is not too hard. He will give out 1530. His final Pokemon is a Milotic, and can be annoying. It is level 43, and powerful. He will give out 1962 Exp! If you beat Wallace, you will get 9300 Yen, TM03, and the ability to use HM07, Waterfall, out of battle.