Covering the Prerequisites
Ensure that you can go to the Sky Pillar north of Pacifidlog Town. You won't unlock these two areas until later in the game, so if you can't yet go to Pacifidlog town as part of the main quest, you can't get Rayquaza just yet. Pacifidlog town is west of Route 131, and is encountered later in the game than most areas.
Purchase a Mach Bike. If you don't have a Mach Bike, you can't catch Rayquaza at all, as there are weak spots in the floor that will sink you if aren't going full speed on the bike.
Carry at least one Pokémon capable of using the HM move "Surf." You'll need to hit the ocean in order to get to Rayquaza, but this should be common by the time you're ready to fight the beast. If you don't have a Pokémon in your party with Surf, grab one from earlier in your adventures.
Train several Pokémon to at least level 70 to avoid being quickly crushed. Rayquaza is the most powerful natural Pokémon you'll find in the game and is already at lv70 when you encounter it. In order to weaken it enough to capture it, you'll need some Pokémon that can hold their own against a high-level monster. You can get Rayquaza either before or after the Elite 4, it is your choice.
Purchase at least 30-40 Ultra Balls to be safe, or decide to use your one Master Ball. This is probably your best chance to use the Master Ball, which will capture Rayquaza automatically, no questions asked. But if you don't have it anymore, Ultra Balls will do, so long as you have a strong team capable of weakening it first.
Make sure you have a Pokémon with a high-level move that inflicts a status effect if not using your Master Ball. Status-effecting moves that inflict sleep, freeze, or paralyze make it much, much easier to successfully capture the Legendary Monster, and they prevent it from fighting back for a few turns. Note, of course, that the higher-level the Pokémon using the move is, the more likely it will succeed. You can use moves like Sleep Powder, Blizzard, or Thunder Wave to inflict these statuses.
Know that you can't catch Rayquaza the first time you see it. In the main quest, you'll meet Rayquaza the first time you go to Sky Pillar. It'll immediately fly away, but you see it again later when he fights Kyogre and Groudon. In this necessary cut-scene (unlocked by flying to Sootopolis after awakening Rayquaza), Rayquaza appears and breaks up the fight, then flies away. As soon as this is finished, you can return to the Sky Pillar to catch Rayquaza for real. If you haven't gotten this far in the quest, you can't catch Rayquaza.
Capturing Rayquaza
Fly to Pacifidlog town, then surf up to the cave just to the northeast. From the Pokecenter in the middle of town, head up to the upper right, skirting through the small "maze" of rocks to reach the cave just northeast of town.
Use the Mach Bike to skirt over the cracks in the floor, getting to the top of the Sky Pillar. The Sky Pillar is a small stage, with two doors on the top of the screen. Use them to move up to the top layer. Whenever you see cracks on the floor, use the Mach Bike to quickly skate over them without stopping. You'll fall through if you try to walk or stop. The Sky Pillar stages are filled with strong Pokemon, but they can be avoided if you use a Max Repel. This is a good way to save your Pokemon's HP for the big battle with Rayquaza later.
Save the game at the top stage before fighting. You only get one chance to catch Rayquaza, so you need to make sure you save in case you fail the first time. If it escapes, defeats you, or faints, you're out of luck. That is, unless you can re-load the save right before the fight.
Weaken Rayquaza to the lower yellow or red section of its health bar. Moves like "False Swipe" and "Tackle" are good for dealing only a little damage at a time, preventing you from accidentally knocking it out and never catching Rayquaza. If you're throwing the Master Ball, toss it out on the very first turn. It will capture Rayquaza automatically for you!
Put it to sleep, paralyze it, or freeze it before throwing your Ultra Balls. Throw down one of these status-affecting moves, then just start chucking. Keep in mind that Ultra Balls don't get better the more you throw them—it ultimately depends on the Pokémon's HP going down in order for the catch rate to become more likely.
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