Joe Higan wordt benaderd door FBI-agenten Mike en Emma om te helpen bij het onderzoek naar de moord op zijn vrouw en zoon.

Higan komt erachter dat een reeks recente moordslachtoffers allemaal ontmaskerde oud-ninja's waren en zweert zijn vrouw en zoon te wreken.

Yamaji onderzoekt vragen over Higans overleving. Ondertussen bundelt Mike zijn krachten met Higan en Emma om hun eigen onderzoek naar AUZA te starten.

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.

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.

The CEO of AUZA dreams of taking total control of the country's energy infrastructure using Yamaji's ninja organization. Emma makes it her personal goal to stop them with Higan's help. Meanwhile, Jason and Mike are still on the run.

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.

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.

Dilly adheres to her original orders and protects Joseph by choosing to fight Yamaji. Higan has a surprise visitor who begs him to put an end to the contradictions of the ninja clan. Meanwhile, Mike has been captured at the FBI offices.

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