The altar is first seen underwater at the start of the game after the player has been shot down by the Pokémon Pinchers. After falling underwater and losing their Capture Styler, they chase a Mantyke to obtain it back. The Mantyke then ends up leaving it at the altar, where the player picks it up before they move away because of the approaching submarine.
Later in the game, players return here after obtaining the Rainbow Grail (Japanese: にじのせいはいRainbow Grail) in Rasp Cavern. After placing the grail on the altar, the altar lifts up to the sky, where Ho-Oh comes to challenge the player. In order to continue the storyline, players must use the Ranger Sign given after the battle so that Ho-Oh would destroy the barrier surrounding the Sky Fortress. Using the Ranger Sign again here at the altar later on allows players to battle Ho-Oh once again.