Red is not in Mt. Moon; he is at the top of Mt. Silver.
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First off, the Red Orb has nothing to do with the Ruins of Alph on Pokemon Heartgold or Soulsilver. The Red Orb is used at the Embedded Tower to summon Groudon. This Pokemon can only be obtained in Pokemon Soulsilver.
He disappears until you beat the Pokemon league again.
you get it after catching or defeating red gyarados
In SoulSilver, Mr. Pokémon will give you the Exp. Share in exchange for the Red Scale that you had received after defeating or catching the Red Gyarados.
I think it's beat red