Teppei ("Tepp") Takamiya is the caretaker of a farm located in Kamui Island, north of Japan. His older brother, Kotarō Takamiya, leaves to study robotics in Germany and becomes one of the most brilliant scientists in the world.

Five years later, the two brothers reunite at a robotics convention in Mechatopia, China, where Kotarō is to announce his latest breakthrough in artificial intelligence. The convention goes awry when Kotarō is captured by the malevolent Machine Empire and taken to "The Area", a mecha base hidden within the sandstorms of the Gobi Desert.

By the means of a mysterious weapon called the Messiah Fist, a cybernetic gauntlet with various technological powers and options, Teppei manages to pursue the kidnappers by grappling onto their "transport", a giant insectoid mecha that is later revealed to be one of the Machine Empire's prized AI machines (known as a B't). Upon reaching the Area, Teppei is attacked by Metalface, one of the Empire's soldiers. Unable to win, Teppei is thrown, bleeding, in the Empire's junkyard. His blood reaches the trashed body of X, who was once considered one of the strongest B't of the Empire, and the disgruntled B't awakens. Faced with unanswered questions and imminent destruction, X reluctantly saves Teppei, and the pair flee the Area with soldiers of the Empire in hot pursuit.

Meanwhile, inside the Area, Kotarō discovers that he has been summoned by another of the Empire's soldiers, Major Aramis, to find a way to stop the ultimate B't - a creation known as Raffaello (ラファエロ) that has begun a terrifying and uncontrollable evolution.

As the series unfolds, the headstrong X and equally brash Teppei develop a brotherly bond, squabbling as much as they look after each other. They slowly uncover the Machine Empire's diabolical plan as they travel through strange lands and battle other B'ts loyal to the Empire, all the while trying to save Kotarō and to resolve the mysteries of their intertwined past.