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.

裏稼業で働く孤独なヤクザの辰巳は、ある日元恋人・京子の殺害現場に遭遇する。 一緒にいた京子の妹・葵とともに命からがら逃げる辰巳だったが、最愛の家族を失い、復讐を誓う葵は京子殺害の犯人を追う。 葵に振り回されながらも彼女を助ける辰巳は事件の真相に迫っていくのだが...