Rayquaza is a Legendary Pokémon, in comparison to which the Elite Four or any other trainer you've faced so far seem like just schoolchildren. Capturing it is a two-step process, as you won't be able to catch it when you first spot it. However, once you have awakened it and seen it in action in the city of "Ceneride", you can return to the spot where you first saw it to proceed with its capture.
Steps
Part 1 of 2: Preparations for the Capture
Step 1. Make sure you visit the "Tower of Heaven" located in the north side of the city of "Orocea"
Until you progress through the game you won't be able to reach these two areas. So, if you have not yet reached the city of "Orocea" following the main storyline of the game, you are not yet ready to face and capture Rayquaza.
The city of "Orocea" is located west of "Route 131" and can only be reached in the final part of the game unlike most of the other areas present
Step 2. Buy a "Road Bike"
If you don't have one, you won't be able to catch Ryquaza. This tool is used to overcome at full speed the most yielding points of the floor that is inside the "Tower of Heaven", which faced on foot would yield miserably.
Step 3. Bring at least one Pokémon that knows the "Surf" move
In order to reach Ryquaza, you need to sail the ocean. In any case, you should already be in possession of this move when you are ready to take on this Legendary Pokémon. If there is no Pokémon on your team that knows the "Surf" move, get one from your previous adventures.
Step 4. Train several Pokémon to get them to at least level 70, so that they are strong enough to resist during combat
Ryquaza is the strongest Pokémon you can encounter in the game, and when that happens, it will already be level 70. To weaken it enough to be able to catch it, you need to use Pokémon that can stand up to it, so with it same level of evolution.
You can catch Ryquaza before or after meeting the "Elite Four", it is simply your personal choice
Step 5. Purchase at least 30-40 "Ultra Balls" or choose to use a "Master Ball"
If you own a "Master Ball", most likely, this is the best time to use it, as this type of tool is capable of capturing Rayquaza automatically with a 100% chance of success. But if you don't have this type of Poke Ball, "Ultra Balls" will be a great alternative, as long as your team of Pokémon is strong enough to weaken it enough.
Step 6. If you don't have or don't want to use a "Master Ball", make sure you have a Pokémon that knows some state-altering attack moves, such as "Sleep", "Freeze" or "Paralysis"
These moves make it easier to capture Rayquaza, and also prevent him from counterattacking, thus extending the fight by several turns. Obviously, the higher the level of the Pokémon that will use this type of move, the greater the chances of success.
Step 7. Remember that you will not be able to catch Rayquaza the first time you see it
During the game's main storyline, you will encounter Rayquaza the first time you go to the "Tower of Heaven". At this juncture, he will fly away immediately, but you can see him again later when he battles Kyogre and Groudon. In this fundamental cut-scene (non-interactive animated sequence that normally has the sole purpose of narrating the events related to the plot of the game), which is shown flying to the city of "Ceneride" after having awakened Rayquaza, the latter will appear and interrupt the fight and then fly away. As soon as the cutscene ends, you can return to the "Tower of Heaven" to attempt to capture Rayquaza.
If you have not yet reached this point in the game, you are not yet able to capture Rayquaza
Part 2 of 2: Capturing Rayquaza
Step 1. Fly to the town of "Orocea", then use the "Surf" move to reach the cave on the northeast side
From the Pokémon Center that you find in the middle of the city, head to the upper right area of the map, then go through the small maze of rocks to be able to reach the cave located to the northeast of the town.
Step 2. Use the "Racing Bike" to overcome the sagging points of the floor of the "Tower of Heaven" and be able to reach the top
The "Tower of Heaven" is a scenario of the game placed at the top of the screen and characterized by two doors. Use them to reach the top level of the tower. Whenever you notice saggy spots in the floor, use the "Road Bike" to overtake them at full speed, without ever stopping on them. If you attempt to overcome these points on foot or if for some reason you stop, you will fall below.
The levels of the "Tower of Heaven" are filled with very treacherous wild Pokémon, but if you wish you can avoid all fights by using a "Max Repellent". This is a great way to save your Pokémon's health points for the next big fight with Rayquaza
Step 3. Once you have reached the top level of the "Tower of Heaven", save your game progress before starting the fight
You only have one attempt to capture Rayquaza, so you need to be sure you can try again in case you fail; that's why it's imperative to save your game progress once you get to this point. Should Rayquaza escape, defeat you or KO you, you will have no other chance to catch him, unless you can reload the game by finding yourself exactly in the spot before the fight begins.
Step 4. Weaken Rayquaza until its health bar reaches the yellow or red section
Moves like "False Swipe" and "Tackle" are great for dealing a small amount of damage each turn of the fight, without running the risk of accidentally knocking it out (which would prevent you from catching it).
If you have decided to use a "Master Ball", do it in the first round of the fight. This way you will automatically have a 100% chance of catching Rayquaza
Step 5. Before throwing your "Ultra Balls", use some moves that can drop Rayquaza into a "Sleep", "Paralysis" or "Freeze" state
What distinguishes "Ultra Balls" is that if the first one you throw fails, the next ones have a greater chance of success. Even if the first "Ultra Balls" you used didn't work, don't think you should weaken Rayquaza any further. Keep holding it in a "Sleep" or "Freezing" state, then keep throwing your "Ultra Balls" until you can catch it.
Advice
- Contrary to what many people think, there are no particular tricks that can increase the chances of being able to catch a Pokémon. Only "Status" alterations and Poke Balls can change this aspect of the game.
- A "Master Ball" guarantees 100% capture of a Pokémon.
- The "False Swipe" move can be used to safely reduce Rayquaza's health level, down to 1 HP (Health Point), without the risk of knocking him out. You can also use the "Super Fang" move for this purpose.
- If you are playing the Game Boy Advance version of Pokémon Emerald by emulating it on a computer, you can save your game progress and try to catch Rayquaza using any Poke Ball without harming it by simply trying to put it to sleep.
- Rayquaza can also appear as a "Shiny Pokémon" (at the start of each fight, these pokemon are able to change their color from the normal version) just like any other Pokémon. However, the odds of encountering a "Shiny Pokémon" are extremely low: around 1 in 8,192.
- To reach the upper floors of the "Tower of Heaven", you must necessarily use a "Road Bike", as the floor is characterized by very fragile and yielding sections that otherwise would make you fall to the lower floors.
Warnings
- Rayquaza has excellent attack moves: "Outrage", "Flight", "Extreme Speed" and "Rest" (all Legendary Pokémon have this last move). Make sure you're ready for a fight.
- Remember that all three Legendary Pokémon of land, sea and air have reached level 70.
