You need a Kyogre and Groudon from the HG/SS games (ones from Ruby/Sapphire don't count). If you then talk to professor oak he will give you a Jade Orb which will make Rayquaza appear at the Embedded Tower.
To get the Blue Orb if you don't have it, you need to talk to Mr. Pokemon after getting the National Dex and one of the Kanto starters from Prof Oak. The Red Orb is only obtainable in SoulSilver.