Play the story until Teams Magma and Aqua awaken Kyogre and Groudon. This occurs towards the end of the story, before you take on the last Gym to get the Rain Badge. Team Magma and Team Aqua will accidentally awake these Pokémon in the Seafloor Cavern after you pass through Sootopolis City for the first time. As long as you play through the story, you won't be able to miss this event. You can have Goldeen learn Waterfall by leveling it up to Level 38, but you'll still need the Rain Badge in order to use it outside of battle to climb waterfalls.
Use Fly to head back to Sootopolis City. You can do this as soon as you exit the Seafloor Cavern after Kyogre and Groudon are awakened. You'll see the two Legendary Pokémon fighting in Sootopolis City, causing the severe weather changes.
Talk to Steven in Sootopolis. You'll find him outside of the Gym, which is closed for now due to the Legendary battle. Steven will take you to the Cave of Origins, where Wallace is waiting.
Talk to Wallace in the Cave of Origin and say "Sky Pillar" when prompted. This is the location of Rayquaza, which you'll need to awaken in order to stop Kyogre and Groudon.
Get the Mach Bike in Mauville City. You'll need the Mach Bike in order to make your way to the top of the Sky Pillar. You can Fly to Mauville and get one from Rydel's Cycles if you don't have it yet.
Fly to Pacifidlog Town. This will be the quickest way to reach the Sky Pillar. If you prefer to take the long way, you'll need to Surf from Route 126 out of Sootopolis all the way to Route 131. You may not have visited Pacifidlog City yet, in which case you'll need to surf from Route 126 to Route 131, passing through 127, 128, 129, and 130 on the way. Make sure to visit Pacifidlog to the west of Route 131 so that you can Fly there easily later. You may want to go the long way and do some training, as well as catch a very useful Wailord on Route 129. This is the only place in the game that you can get one.
Leave Pacifidlog to the east on Route 131. Surf to the north end of Route 131.
Enter the Sky Pillar. Wallace will appear and say that he's unlocked the door to the Sky Pillar.
Make your way up the Sky Pillar. You'll need to use your Mach Bike to cross the cracked sections of the floor. The Sky Pillar is five floors, so you'll be battling quite a bit to make it to the top. On the fourth floor, you'll need to fall through the second cracked section along the top of the big gap. This will drop you into a blocked area on the third floor. Head up the stairs back to the fourth floor, and then up the stairs again to the fifth.
Approach Rayquaza to awaken it. It will shake the Sky Pillar and fly off to Sootopolis City.
Use Fly to return to Sootopolis City. You can use Fly from the roof of the Sky Pillar. When you arrive at Sootopolis, you'll see Rayquaza drive off Groudon and Kyogre.
Surf to the Sootopolis Gym. Archie and Maxie will realize that they've done a bad thing, and return the orbs they stole to Mt. Pyre.
Talk to Wallace outside the Gym. He will give you HM07 Waterfall, and inform you that you'll need to earn the Rain Badge by defeating the Sootopolis Gym Leader in order to use it. After giving you Waterfall, he will move aside and allow you to enter the Gym.
Prepare your party to take on the Gym. Juan, the Gym Leader, uses a Water-type party, with a Level 46 Kingdra as his most powerful Pokemon. Try to have a Dragon-type in your part to quickly take down the Kingdra, and plenty of Grass-type and Electric-Type Pokémon to do heavy damage to the Water Pokemon.
Complete the first ice puzzle. You'll need to walk across the ice in the correct order to make the staircase to the next section appear. Start from the top of the stair case and move the following directions to complete the first puzzle. If you mess up, you'll fall into the basement and be forced to fight trainers. ↑1, ←1, ↑1, →2, ↑1, ←1
Complete the second puzzle. Start from the top of the second staircase and perform the following steps: ↑1, ←3, ↑2, →2, ↓1, →2, ↓1, →2, ↑2, ←3
Complete the final puzzle. This last puzzle is fairly complex, but if you do it correctly you'll end up right in front of Juan: ↑1, ←5, ↑3, →1, ↓1, →1, ↓1, →1, ↑2, →1, ↓1, →1, ↓1, →1, ↓1, →1, ↑1, →2, ↓1, →1, ↑3, ←2, ↓1, ←1, ↑1, ←2
Defeat Juan and earn the Rain Badge. This badge will allow you to use Waterfall outside of battle to climb waterfalls throughout the world. You can now teach HM07 to whichever Pokémon that you want to have it. It is usually best used on the same Pokémon that knows Surf. You'll need Waterfall to access the Elite Four in Ever Grande City.
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