FBI-agentit Mike ja Emma lähestyvät Joe Higania saadakseen apua tämän vaimon ja pojan murhatutkinnassa.

Higan saa tietää, että hiljattaiset murhauhrit olivat kaikki entisiä ninjoja, joiden peiteroolit paljastuivat. Hän vannoo kostavansa.

Yamaji vastaa Higanin selviytymistä koskeviin kysymyksiin. Mike yhdistää voimansa Higanin ja Emman kanssa aloittaakseen AUZAn tutkimisen.

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.