Story:Pokemon Guava and Mango/Whirl Islands

Much as they were in the original Johto games, the Whirl Islands exist in Pokemon GM as a post-game odyssey for the player to explore once the main story is completed and the Whirlpool move is available.

As explained in Pokémon SoulSilver, the Whirl Islands used to be one large island. At some point in time, there were two countries fighting over the island. Lugia, the guardian of the island, got upset and cast lightning bolts to tear the island into four pieces. It then disappeared into the deep end of the waterfall basin, longing for the invisible trust between people and Pokémon to manifest once more.

After the story events that transpired in the Whirl Islands with Lugia intervening in conflicts with the Consortium, the legendary Pokemon returns to the islands and enters a deep hibernation state to recover its expended energies. In the subsequent aftermath, Cianwood Gym Leader Millennia disappears suddenly from her gym, leaving the running of it to Berah Ronah, Gym trainer and second-in-command. (Spurned by his Leader's disappearance, trainer Ragya-Vara disembarks in the post-game as well, and goes on to assist at the Centre of the Hand and Land with cooking shenanigans.)

In the postgame the player is able to explore the Whirl Islands and investigate Millennia's disappearance. Throughout their journey and observation of ruins uncovered by the chaos, the player is able to piece together that Leader Millennia has discovered an entire underwater temple built in reverence of the legendary Sea Witch.