In FireRed and LeafGreen, like Birth Island, Navel Rock is invisible on the Town Map by default, only appearing when the player first arrives there. This is in contrast to the other Sevii Islands, which do appear on the Town Map. In Emerald, it never appears in the PokéNav's map.
Lugia dwells on the lowest floor while Ho-Oh dwells in the sky above the island. When the player reaches the very top of the rock, Ho-Oh flies down to meet them.