The game's story primarily focuses on the exploits of the space-faring organization known as Oracle, who uses Photons to traverse the universe and seek new planets for potential colonization while simultaneously suppressing the threat of the Falspawn, alien beings created by evil entities known as Dark Falz that only exist to destroy the universe. Oracle is split between a Mothership, housing the fleet's central core, and a massive fleet of spaceships that contains all civilian entities and the fleet's prime military and exploration department known as ARKS (Artificial Relicit to Keep Species).

Initially, ARKS is sent to investigate activity on three planets: Naverius, a planet whose ecosystem was primarily forest before much of the planet became locked in eternal winter, Lillipa, a desert planet inhabited by rabbit-like natives known as "Lillipans", and Amduskia, a bifurcated planet with a volcanic core surrounded by a mass of floating islands inhabited by humanoid dragonfolk. Later story arcs feature the planet Wopal, an ocean planet, and Harukotan, a planet in the shape of a taijitu inhabited by two opposing races. In EPISODE 4, exploration expands to encompass a fictional counterpart of Earth located in an alternate dimension, and in EPISODE 5, an alternate dimension known as "Omega" located within a black hole becomes the focal point of the story.