Somewhere on the beautiful planet Aira, in a small village Toto lives a young boy named Rei. Rei possesses unique spiritual powers, using which he can heal diseases. One day, Rei is ordered to go to Tristan, the Royal Capital, where he is needed. This seems like a simple journey; but shortly afterwards Rei meets the cat Nyan, who got stranded on Aira following a hostile encounter with Burakki, Gorokki, and Chorokki, intergalactic feline travelers with unknown agenda. The boy realizes that his powers might be needed to aid the heroes of the previous Cosmic Fantasy installments, and deal with the mysterious Garudo, who recently came to Aira, plotting an evil scheme.

Cosmic Fantasy 3: Bōken Shōnen Rei is the third installment of the Cosmic Fantasy sci-fi anime role-playing series. It is a traditional Japanese-style RPG with turn-based, first-person perspective combat. Enemies appear randomly. Rei and other party members can execute various types of physical attacks and techniques in battles, each with its own strengths and weaknesses. The game features anime-style cutscenes with voice-overs. Instead of separate locations tied by a traditional "world map", the game has a continuous world, in which locations are seamlessly connected to each other.