The game opens with a dreamlike sequence: the player is asked fragmented questions about "that day" — an event whose significance will not become clear until much later. After sketching a scene hinting at this mystery, the player watches Heather, a character from the first game, tormented by nightmares before being abducted by a darkness connected to a red jewel pendant she wears. The mastermind is Wilfre, who scatters the Raposa villagers, drains the village of color, and takes Heather captive. The surviving Raposa escape aboard a massive turtle summoned by the Creator and journey through Watersong, Lavasteam, the Galactic Jungle, and Wilfre's Wasteland — a region that fuses elements of all three — to reunite their people and stop Wilfre, while slowly piecing together what "that day" actually was.