Kyohei Aizawa, an assassin for a covert non-governmental espionage group in Japan called "四十九" or "SEEK", is grieving over the loss of his girlfriend from a tragic plane accident. The leader of “SEEK”,Ryo Mikumo, contacts him for an emergency mission; save a fellow agent, recover a new highly explosive liquid called “RDX@“, stop a ruthless Yakuza leader, Sojiro Kotsuki, and his gang before they take over Japan. Although the Ninjas were thought to have disappeared...the new breed of assassins live on helping to protect Japan and all that is right; the Ninjas are coming soon.

The 1923 Kanto earthquake sparks fears of a Korean uprising in Japan. Many anti-colonial and leftist activists are arrested, including Fumiko and her partner Yeol. Accused of a plot to assassinate the Crown Prince, they are sentenced to death, later reduced to life in prison.

British RAF Wing Commander James Wright is captured by the Japanese during WWII and forced to fight in brutal hand-to-hand combat. The Japanese soldiers get more than they bargained for when Wright’s years of martial arts training in Hong Kong prove him to be a formidable opponent.

The world is now on the brink of World War III, a terrorist group posing as Russian extremists want to destroy Japan. Kyohei Aizawa and SEEK must stop them. The ancient art of the ninja is still Japan's ultimate shield and only hope.