Ninja Resurrection follows the adventures of a young Jubei Yugyu on special assignment to the General of the Toyotomi clan. The volume begins with the introduction of Christianity in feudal Japan and how a young boy becomes the next Saviour. After being ousted for his religion, he continues to deliver his teachings to the world and eventually builds up a large following. Religious wars and persecution follow. Thus enters Jubei and his small group – sent to assassinate him since he is safely tucked away behind his fortress.