After his family was brutally attacked by a gang of masked assailants, Joe Higan 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.
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.
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.
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.
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.
A mysterious benefactor warns Higan that it's impossible for him to infiltrate AUZA City without any help. Meanwhile, Mike and Emma walk away from the accident with light injuries and relaunch their investigation into AUZA and the ninjas.
Emma and Jason combine their efforts to launch a hacking attack on AUZA, which results in them obtaining top-secret information. Meanwhile, Mike and Higan fend off a squadron of mercenaries sent by AUZA to stop them.
Higan mourns Emma's death when a letter challenging him to a duel arrives from Zai. Mike and Jason want to leak the data they hacked from AUZA to the public but discover they can't due to Emma's external memory drive being encrypted.