Defeat the Elite Four and the Champion. Before you are able to find and capture Kyogre, you'll need to beat the main game by defeating the Elite Four and the Champion. You'll have to defeat all of them in one go, or else you start over, so make sure you're prepared. Stock up on Hyper Potions. These are the most cost-effective potions in the game. Most Pokémon won't have more than 200 HP, making these just as effective as a Max Potion for much less money. Stock up on Revives as well. You'll want to be able to bring back your key Pokémon between rounds. Make sure your party is Level 56 or higher. Every Pokémon in your main party should be at least Level 56 before you take on the Elite Four. If you have Rayquaza, use it in this battle since it is much higher level than the Elite Four's and Champion's Pokemon. Save after you beat each Elite Four member. This will allow you to reload instead of starting over from the beginning. See How to Beat the Elite Four on Emerald for more details.
Level up your Pokémon to at least Level 70. Kyogre is a Level 70 Pokemon, so you'll want a party that can take a beating and keep fighting. Leveling your entire party will take a while, so you can probably focus on just raising a few of your most powerful Pokemon. Rayquaza will be a big help, since it is Level 70 when you catch it. Grass- and Electric-type attacks will help quickly lower Kyogre's health. You'll need to have a Pokémon that knows Dive in order to access the cave that Kyogre is in.
Stock up on Net Balls and Timer Balls. Net Balls are the most effective Poke Balls to use against Water-type Pokemon. Try to have at least 40 of them in your bag. Timer Balls are also very useful, and are more effective than Net Balls after the 30th turn. Make sure to do all of your prep before you go hunting Kyogre, as it won't stay in one place for very long. If you have your Master Ball, you can use it on Kyogre to catch it instantly. You only have one though!
Head to the Weather Institute on Route 119. Once you are given control of the game after beating it, use Fly to quickly head to Fortree City. Head west onto Route 119 and enter the Weather Institute in the northwest corner.
Talk to the Scientist to discover Kyogre's location. Kyogre's location varies, and if Groudon is active you'll have to either catch it first or wait for the weather to change. If the scientist says that there is "Heavy downpour" on a certain route, this is where you can find Kyogre. Possible routes include Route 105, Route 125, Route 127, and Route 129. If the scientist says that there is a "drought" on a certain route, that means that Groudon is active. You'll need to either go to this location to catch Groudon, or wait for the weather to change and then speak to the scientist again. See How to Catch Groudon for more details.
Head to the route with unusual rain. Fly to the nearest city and then head to the route that the scientist told you about. You'll notice rain and lightning as you walk around.
Surf the water and look for the dark spot. A dark spot will appear in the water when it is raining. This spot changes depending on the location, so you'll just have to Surf around until you find it.
Dive into the dark spot. Use Dive when you're on the dark spot in the water, and you'll end up in an underwater cave.
Enter the cave entrance. At the back of the underwater cave, you'll see an entrance. Swim through it.
Surface into the Marine Cave. Once you pass through the entrance, you'll be prompted to surface. This will take you to the Marine Cave.
Save your game. Create a save here before fighting Kyogre. This will allow you to quickly reload in case you accidentally knock out Kyogre or your party gets wiped. If Kyogre gets knocked out, it will disappear forever, so you'll need to reload your saved game.
Start the fight with Kyogre. Make your way through the cave and approach the pool that Kyogre is in. It will swim up to you and the fight will begin.
Lower Kyogre's HP to the red zone. Use Grass- and Electric-type moves to take large chunks of Kyogre's health. You'll want it in the red before you start trying to use Poke Balls. If you want to use your Master Ball to catch Kyogre, simply throw it at the start of the fight and Kyogre will be caught instantly. Remember, you only get one Master Ball.
Start throwing Net Balls once its health is down. Net Balls will give you the best chance to catch Kyogre, so start throwing them once its health is in the red. Throw a ball every turn that you can. Kyogre has a move that will put it to sleep and completely restore its health. Don't be disheartened! Your chances of capturing it actually increase while it's asleep, so keep throwing balls. Once it wakes up, take its health back down.
Throw Timer Balls after 30 turns. Once 30 turns have passed, Timer Balls become more effective than Net Balls. Make the switch to improve your chances.
Reload your game if you run out of Pokémon or Kyogre gets knocked out. Kyogre has a move that that damages itself as it damages you. This means it may knock itself out. When knocked out, Kyogre disappears forever. If this happens, you'll need to reset and reload your game. You'll also want to reload if you get knocked out, since Kyogre will move and you'll have to start all over.
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