Kazuki Muto was transformed into a Buso Renkin by Tokiko after he was killed by a homunculus, a flesh-eating monster. Now, Kazuki and Tokiko are racing against time to find the creator of the homunculi before the one that is lodged at Tokiko's waist reaches her brain and transforms her into a homunculus. Unknown to them, the person they seek is a student at Kazuki's school.

Upon arriving at the headquarters of the L.X.E., the Alchemist Warriors learn of the League's plot to attack the high schoo. They immediately head over there, only to discover that the school is surrounded by Dr. Butterfly's humunculus soldiers. Plus, they'll have to face the students, too!

Kazuki and Tokiko are on the run from the hunters of the Alchemist Warriors! Tokiko, now reduced to the size of a doll, fights alongside Kazuki and Gouta as they take on three of the hunters and Captain Bravo himself, who's past is finally revealed! As Kazuki and Captain Bravo's battle draws to a close, another Warrior Chief appears, as well as a man calling himself the Great Warrior Chief. What will it mean for Kazuki and his friends?

The Alchemist Warriors head for Papillon Mask's hideout in order to stop him from carrying out his mission to destroy the entire world.