PokéBase - Pokémon Q&A
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You need to bring the Jade Orb to Embedded Tower.

To get the Jade Orb, the player must show Professor Oak a Groudon from SS and a Kyogre from HG (any migrated Pokemon will not work). Once you have the Jade Orb, bring it to Embedded Tower and fight Rayquaza.

To get Kyogre and Groudon, the player must talk to Mr. Pokemon after getting the National Dex and a Kanto starter. In SS, you will get a Red Orb, which allows you to see Groudon in Embedded Tower. In HG, you will get a Blue Orb which allows you to see Kyogre. You will have to trade to get both Pokemon in the same game. Once they are both in your party, Professor Oak will give you the Jade Orb. Remember, the Kyogre and Groudon must be from HG/SS, and any Pokemon received otherwise will not be accepted by Oak.

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too much un needed info.
Not necessarily. Since connorg asked how to get Kyogre and Groudon, I added that in.
yeah right Fizzcube.
where is Mr.pokemon?
He is in the northernmost house on Route 30.
Does anybody have a HG Kyogre for trade? I have a Mewtwo, Ho-oh, Heatran, Giratina (Lv.72 or 13), and a Shiny Gyarados or Lv.40 Magikarp.
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You must have kyogre and groudon in your party. Then go to embedded tower.

Source - Experience

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OK how do I get those two?
Wouldn't it be much easier just to look at Fizzcube's answer? But you need to get Kyogre and Groudon from Soulsilver and Heartgold, so you will have to trade with a friend or get a different HG/SS game.