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.
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.
In the manga
In PS611, the Embedded Tower was revealed to be the place where the Pokémon Association had found and captured Rayquaza years earlier. This operation had unintentionally also led to the death of Aster, a Draconid lorekeeper, who had tried to defend Rayquaza from being captured by Mega Evolving it. As a result of Aster's death, her successor, Zinnia, had sworn a vendetta against the Devon Corporation, which had participated in the capture operation.
- If the Blue OrbSS or the Red OrbHG is obtained with an external device and brought to the tower, the appropriate etchings will appear on the floor. The Pokémon itself will not appear, however.
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