KyogreHG/GroudonSS appear at the Embedded Tower when the player is in possession of the Blue OrbHG/Red OrbSS (which can be received from Mr. Pokémon after the player has obtained a Kantostarter Pokémon in Pallet Town after defeating Red). If a Kyogre and a Groudon that are caught at the Embedded Tower are both shown to Professor Oak, he will award the player with the Jade Orb, which causes Rayquaza to appear at the Embedded Tower; Professor Oak will not give the Jade Orb if shown Groudon and Kyogre from any other location.
Appearance
The appearance of the interior changes depending on which of the trio occupies it at the time. If Kyogre is in the room, the markings on the floor will be red and depict the pattern on Kyogre's fins. If Groudon is there, then the markings will be blue and show Groudon's arm patterns. If Rayquaza is occupying the Embedded Tower, then the markings will be yellow and represent those on Rayquaza's body.
History
A long time before the events of HeartGold and SoulSilver, the Embedded Tower was an enormously tall tower built by people who came from the Hoenn region. Its peak was said to touch the sky, and part of it was embedded into the cliffs of Route 47, running deep underground into the ocean— thus connecting the land, the sea, and the sky.
A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.
If the Blue OrbSS or the Red OrbHG is obtained with an external device and brought to the tower, the etchings will appear on the floor. The Pokémon itself will not appear, however.