Rayquaza
Go to Sky Pillar, and press A in front of Rayquaza (who is at the top of the pillar).
Go to Sootopolis City. A cutscene should play. When it's is finished, press A in front of Rayquaza (at the Sky Pillar again), and then go into battle.
Use level 80+ Pokémon (Rayquaza is level 70), and you should have 50+ Ultra Balls (or, if you still have it, your Master Ball), and then make Rayquaza fall asleep. Paralysis is also an option, but Sleep lasts longer. If you have it, attack using False Swipe.
When Rayquaza's health bar turns red, throw Ultra Balls balls frequently. If you're using your Master Ball, you probably need to lower the health to about half, but throwing a Master Ball when Rayquaza's health is red will almost always capture it.
Groudon
Defeat Team Magma so that they release Groudon from captivity.
After defeating the Elite Four, go to the Weather Institute, and talk to the scientist on the topmost floor. He will tell you the route Groudon is on (randomized).
Go to the route the scientist mentioned (Groudon should be in a cave). Make sure to bring level 55+ Pokémon, 50+ Ultra Balls, and 1 Master Ball (if you still have one). Go into battle. Put Groudon to Sleep, and then use Ultra Balls or a Master Ball.
Kyogre
Defeat Team Aqua so that they release Kyogre.
Use Dive to get to Kyogre, because it is in an underwater cave. Bring level 55+ Grass Pokémon, because Kyogre is an ice/water type Pokémon. The same method applies mentioned above: put Kyogre to Sleep, lower it's health to red, and keep throwing Poké balls.
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