Where Do You Find Rayquaza In Soul Silver?

You cannot find it unless you have both Kyogre and Groudon caught by yourself...Then you visit Professor Oak's Lab and then he will give you the "Green Orb"to catch the Rayquaza a the same place...Also I have Groudon and Kyogre twice..but not caught...xD

You get rayquaza by getting the red orb from the man in the brown suit at mr.pokemons house. The house where you first met prof. Elm.
But first you have to get the national pokedex from professor oak after beating the elite four.
And then you have to beat red on top of mnt. Silver after beating all the eight gym leaders in kanto as well.
After you obtain the orb you you go to route 47 the cave in cinawood. If you have ss you will get groudon or if you have hg you will get kyorge. But you have to get one of them over trading so if you get groudon you have to find a way to kyorge from trading. Or the other way around.
After you have groudon go see prof oak and he"ll tell yuo about the tower and tell you once you have groudon and kyorge he will give yuo the orb to reach rayquaza!