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.