《忍者刺客49》Kyohei Aizawa, an assassin for a covert non-governmental espionage group in Japan called "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.