In the village of Tsuda, where JSA rookies undergo training and retired veteran spies live as instructors, a sudden incident occurs—the villagers vanish without a trace. Agent 03 is assigned to investigate. Walking through the deserted village with not a single person left behind, 03 senses an eerie presence lurking somewhere. While washing off sweat at an open-air bath, she notices a dark shadow creeping up from behind. The figure signals an attack by a sinister ninja clan. Though 03 temporarily escapes the scene, she deliberately reveals herself again, knowing full well the ninjas are still hunting her.