After getting the earth badge go to mr. Pokemon and he will give you a red orb if you talk to him. what you do with it later is unknown to me.
Well first I should clear up that the Red Orb is for SoulSilver, and the Blue Orb is for HeartGold, but you must defeat Red in order to get it.
in the cave of origin or the top of mt pyre
You need to beat the game twice and then you need to beat Red at Mt.silver then you can get the blue orb from Mr Pokemon in his house.
after professor oakgives you another starter when you get all 16 badges
After you have beaten red, go to professor oak. get a kanto starter. use the magnet train or fly to jhoto. go to Mr. Pokemon's house and he will give you the red orb
for starters, have you defeated Red? If not, you need to go do that first. Yeah. I know. :( You also need to have gotten all 16 gym badges as well.
Get all sixteen badges and defeat red
-sigh-...again with the stupid questions >( Okay, I'm going to try and answer this question without venting... Mr. Pokemon doesn't give you the Blue Orb in SoulSilver, he only gives you the RED ORB. Then you have to find someone with HeartGold (Good luck with that). Ask if they have caught Kyorge. When you have the traded Kyogre, go back to Mr. Pokemon, he'll give you an orb that'll allow you to catch Rayquaza
blue orb for groudon and red orb for kyogre
In HeartGold you get a blue orb and in SoulSilver you get a red orb
in soulsilver you get the red orb in heartgold you get the blue orb
You can only get the Red Orb in in Pokémon Ruby; in Sapphire, you get the Blue Orb, while Archie, the leader of Team Aqua, takes the Red Orb.