Kyogre goes in the sea.
You don't get Kyogre in Ruby; instead, you get Groudon. If you want Kyogre, you have to trade one from a Sapphire or Emerald game.
You go to the weather institute and talk to the scientist guy and you go to drought cave for Groudon and where you get the regi's for Kyogre
after you beat red,go to the embedded with the blue orb,and kyogre will appear
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go to the weather institute in emerald and go to the second floor to far left and a man will be standing there he will tell you where to catch groudon and kyogre.
To get kyorge you need to defeat red. then go and talk to mr.pokemon. he will give you a blue orb. then go to embedded tower and kyogre will be there.
To get rayquaza, you need to get groudon+a kyogre and then go to the man where you got togepi from and then you will receive a green orb then go to the place where kyogre/ groudon was and then catch it. I've got groudon and now all I need now is kyogre. I also caught zapdos with one ultra ball
u do not need a crystal to catch kyogre, trust me. simply, when the time has come find sootopolis city and go into the cave of origin. go trhough the levels, then you will battle some people then you can catch kyogre.
go to stormy sea and on the 40fl you will find kyogre P.S. you will need dive
Go to stormy sea and there are forty floors till u get to kyogre
You can try to get the other kind of orb which will get you kyogre and after you get kyogre you can go back there and get rayquaza.
To catch kyogre without masterball buy 20 ultraballs and 1 healball and go to the embeded tower if u have blue orb you can go if you don't you cannot go because you need blue orb to catch kyogre then if ur fighting kyogre use healball first before the ultraballs if the healball fails to catch use the ultraballs but you need to attack kyogre before you can catch it i use hydrocannon on kyogre and his hp is red and i use my ultraball and i capture it Hope This Helps