One theme or lesson to be taken from The Master Puppeteer is that of the good side and the bad side of manipulation. Jiro learns that the puppet master manipulates the audience to cause them to feel and perceive even as he manipulates the puppets to do things. Jiro also learns that the master puppeteer manipulates his students so that they will learn the lessons they need to know to be faithful and skilled puppeteers. Jiro also learns that horrible events like famine can be brought about by manipulation.
He also learns the greatest lesson that the double-edged sword of manipulation can be controlled only by following the old samurai code of selflessness. This is an especially important lesson for today when selflessness is seldom thought of. With selflessness, then manipulations by a wise person are for a higher wisdom and turn out to be for others' benefit. Without selflessness manipulations by a self-serving person bring harm and destruction to the other person.