After his family was brutally attacked by a gang of masked assailants, Joe Logan is approached by FBI agents Mike and Emma to help investigate the murder of his wife and son.

Higan learns that a string of recent murder victims were all former ninjas who had their covers blown. Higan goes after the boss ninja and swears to take revenge for his dead wife and son by crushing the organization.

Yamaji addresses questions from one of his lieutenants regarding Higan's survival. Meanwhile, Mike joins forces with Higan and Emma to launch their own independent investigation into AUZA.

Mike uses information from Emma to track down Jason, a former AUZA employee. Elsewhere, after having his first attempt to infiltrate AUZA City stopped by Zai, Higan learns of an alternate route from the mysterious benefactor.

Aska rescues Higan from certain doom and her true identity is unveiled. Meanwhile, Mike learns that he is now wanted by his own agency, the FBI.

As Higan and Lil engage in combat, Higan achieves complete synchronization with his Gusoku Gear, known as "Kamui." Afterward, Yamaji finally orders Zai to eliminate Higan.

Higan wins his duel against Zai, but stops short of killing him. Joseph sends his mercenaries to attack the ninja hideout after cutting his ties with Yamaji. Meanwhile, Mike figures out the key to decrypting the data Emma left behind.

Higan and Yamaji engage in a final battle. Meanwhile, Mike tries to track down Joseph as he tries to flee the country.