Like Professor Oak tells you, if you can bring a Kyogre from HeartGold (it can't be from Pokemon Sapphire, or it won't work) and the Groudon you already have and show it to him, he will give you the Jade Orb.
Thus, you must temporarily trade a Kyogre from HeartGold to your SoulSilver version so you can get the Jade Orb to make Rayquayza appear. Both must be in your party (but don't have to be in the first slot) to get the Jade Orb.
Steven Stone is in Heartgold and Soulsilver because he tells you that Latias or Latios (depending on your version) is flying around and able to be caught.
HeartGold-Latias SoulSilver-Latios After speaking to the people in the fan club in Vermillion City, Steven is stading outside the fanclub. Speak with him and he tells you that a Hoenn legendary is now roaming in Kanto.
After you defeat blue, go to victory road gate and go left. Professor Oak will appear and tells the guard to let you through.
In Heart Gold and Soul Silver:He appears after reaching Kanto for the first timeHe tells you about one of the Lati@s pair while you help out CopycatAfter defeating Red, he will be in Silph Co. to offer you a Hoenn starter pokémon.
Celadon Game Corner.
He gives it to you as a gift for completing the sinnoh pokedex.
Go to lake valor...
He tells you to visit him so he can give you pokemon.
Waterfall is in the Icy Path.Go to Ice path and someone stops you and tells you that he drop something waterfall is in that pokeballyou get waterfall in the ice path
he tells you that you need to get all of the badges from Kanto then he will let you into Mt. Silver
Beat the elite four and ash whos on mt silver(his pokemon are in the low 80s). then it goes on for you. A Person tells you that the missing pokemon was returned and one of the proffesors( im sorry i dont remember which one. the game tells you) lets you choose one of the pokemon from kanto.
You will have to have caught either a Groudon from the Soulsilver Version or a Kyogre from the Heartgold Version.That will happen after you get either the Blue or Red orb from Mr. Pokemon..You might want to see professor Oak first or not.You go to the Embeddied Tower to get them.After you catch the one that is in your version, go talk to Professor Oak, and he will tell you about it.Make certain that the Embedded Tower Pokemon is in the first slot.He tells you that you will also need to get ahold of the other one, and that they will not reveal themselves to a person with a heart of gold or shining silver soul, depending on the version you are playing, meaning you will probably have to trade for the other one, but it MUST BE CAUGHT IN THE EMBEDDED TOWER.after you have both Groudon and Kyogre, probably in first 2 slots, talk to Professor Oak again.Presently I have only 1, but not both, but this is what I heard, so I hope that I am correct.I think when you talk to Professor Oak again with both Emedded Tower Pokemon you will probably be given the Jade orb, and on your way to challenging Rayquaza.Good Luck