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.

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.

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 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.