After awakening Rayquaza at the Sky Pillar and watching it calm Kyogre and Groudon, you can return to the Sky Pillar at any point to battle and capture it.
You will need the Mach Bike to climb the tower the second time, however.
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you need to awaken Kyogre[in team aqua's hideout]Groudon[in team maga's hideout] and Rayquaza[in the sky pillar]
beat the 8th gym
sootopilis city
You might need to open the door to the 8th gym in Pokémon Ruby, Sapphire and Emerald. To do this you first have to awaken Rayquaza.
...... stewen in emerald isn't a elite champion. there is wallace.