Shy has grown up a little after fighting against the 'Amalareik,' led by the mysterious boy Stigma. When she returns to Japan, she meets a girl named Ai Tennouji who has run away from her ninja village. Ai tells Shy that she left the village to chase a member of the 'Amalareik.' Meanwhile, an incident occurs in which Tokyo is suddenly enveloped in a black ball and disappears. The heroes are dispatched to rescue Tokyo.