After 11 years of training with a strange woman named Karen, Teppei is going to see his older brother Kotaro Takamiya at a scientific conference. His preparations for a family reunion, however, are thwarted when a woman named Aramis kills everyone at the conference in order to capture Kotaro. Teppei meets a damaged mechanical horse named B't X on his route to save his brother, who is revived owing to Teppei's blood and is now his ally in the fight to save his brother from the mysterious Machine Empire.