If I go to the sky pillar the second time will I find kyogre,groudon & rayquaza.
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You will find Rayquaza the second time, he will be at level 70, take many Ultra balls with you, a mach bike to get over the holes in the floor, max repels so you don't get interrupted by level 50 Pokemon on your way up there (interruptions stop you getting over the holes in the floor) and Rayqyaza is a Flying Dragon Type. So take suitable Pokemon so you can catch him. Save just before battle, so you can reset if you knock him out. Because it is a one off battle)
If you are looking for Groudon and Kyogre, you will be able to find them both in game, after you have beaten the elite four.
Go to the Weather institute nearby Fortree city (where you were given Castform) and talk to the man you saved there, he will tell you that there is a particularly rainy area in Hoenn (it changes frequently, so go to the route he tells you and look around) and there you will find Marine cave and Kyogre who is a water type and will be at level 70. (you will need Surf and Dive to get there.)
Groudon who is a Ground type, and will be in Terra cave at level 70. But go instead to the place where the weather isn titute worker tells you there is a really sunny patch.
You will know you have gotten there because it will be raining heavily or the sun will be shining brightly.
When you go sky pillar afetr the controversy in sootoplolius has been resolved you can oly get rayqauza at level 70 there and a few other Pokemon such as claydol, altaria, sabelye and golbat at like level 36
After you catch them/kill them once, they'll never appear again, unless you have a cheating device.
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