Oslo send Yuuji to a training camp for child soldiers in an attempt to create a super soldier. Of all the test subjects, only Yuuji survived the brutal training regime and experimental "booster drugs" intended to instill super-human strength. For this reason, Oslo cloned Yuuji, using a girl who had befriended the original Yuuji, Marlin, as a surrogate mother. The strain of child birth at such a young age killed Marlin, but the clone of Yuuji was born.
The clone would not be seen again until he attacked a foreign embassy under the guise of Yuuji himself, framing him for the attack. Yuuji was imprisoned for the crime, and intended to be used as a bargaining chip with Heath Oslo, who threatened to destroy Tokyo with nuclear weapons unless the Japanese government handed over both Yuuji and a supercomputer known as Thanatos.
With the help of his friends from his school at Mihama academy- which the original Yuuji spent a year at while on leave- as well as his old military buddies and Yuuji's sister, who he intially believed dead, Yuuji escapes from both the Japanese government and Oslo's grasp.
The original Yuuji attacks Oslo's base of operations, on the aircraft carrier Tartarus, and engages in combat with his clone. The clone force Yuuji to consume a booster drug against his will, which only serves to infuriate Yuuji. The two of them engage in close combat with firearms, knives, and their bare fists. The original Yuuji wounds his clone with a Glock pistol taken from him, but the clone keeps fighting until Yuuji kills him by stabbing him in the chest with a combat knife.