- Go to Sootopolis City and find Wallace in the Cave of Origin, on the north shore of Sootopolis lake.
- Stock up on healing and Poke Balls before going to the Sky Pillar. Surf to Route 131 and find the Sky Pillar entrance in the upper-right corner of the route.
- Climb the tower and wake Rayquaza. He’ll fly off, but you can continue the quest and return to the Sky Pillar when you’re ready to capture him.
Go to Sootopolis City. In order to unlock the Sky Pillar, you will need to talk to Wallace in Sootopolis City. You will need a Pokémon with the Dive and Surf ability in order to access it. You can get Surf in Petalburg City and Dive in Mossdeep City after beating each of the Gym leaders. You will need to complete the events with Team Aqua that awakens Kyogre before you can continue. Go to Route 126 in the southeastern side of the map. Surf to the south side of the volcano rising out of the water. Dive in a dark spot of the water. Enter the opening on the south edge of the volcano underwater. On the other side of the opening, use dive again to enter Sootopolis City.
Find Wallace. Wallace can be found in the Cave of Origin, which is located on the north shore of the Sootopolis lake. You will need to speak to Steven to the west of the gym in order to get to Wallace. Speaking to Wallace will unlock the entrance to the Sky Pillar.
Stock up before heading to the Sky Pillar. Use the Poke Center to heal your Pokémon and purchase any necessary items and Poke Balls.
Surf to Route 131. The Sky Pillar can be accessed by surfing from Sootopolis City or by flying to Pacifidlog Town and surfing to the east. If you haven't reached Pacifidlog Town yet, stop by so that it gets added to your map. You can then fly to Pacifidlog Town whenever you'd like, which makes getting to the Sky Pillar much easier.
Find the Sky Pillar entrance. The cave entrance to the Sky Pillar is located in the upper-right corner of Route 131. You will need to surf around some rock formations in order to find it. Walk through the cave and out the entrance at the top. Keep walking towards the top of the screen. You will encounter the entrance to the massive Sky Pillar.
Climb the tower. You will need to climb four floors in order to reach Rayquaza. The enemies that you run into in the tower will range from level 30 to level 40. Use this opportunity to capture a Claydoll, as well as a Golbat if you haven't got one yet. On the 3rd floor, you will need to drop down the hole at the dead end. This will drop you in front of some doors you couldn't reach before. Use the left door to reach the 4th floor.
Wake Rayquaza. As your approach Rayquaza on the roof of the Sky Pillar, he will wake up and fly off. You won't have the chance to battle him right now. Instead, head back to Sootopolis City to see Rayquaza stop the battle between the two Legendary Pokémon. Once the battle is over, all three Pokémon will disappear.
Return to the Sky Pillar when you're ready to capture Rayquaza. Once Rayquaza disappears from Sootopolis City, he will return to the top of the Sky Pillar. In order to reach him this time, you will need the Mach Bike from the Bike Shop near Mauville City. Rayquaza is level 70, so make sure that your team is ready for a long fight, and that you have all of the necessary items and Poke Balls. You can use the Master Ball to capture him immediately, but if you don't want to waste it you can whittle his health down and user lower-tier Balls. See this guide for more details on how to effectively battle Rayquaza.
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