Even though Haruto reveals that Koyomi is Fueki's daughter, the group keeps their mission to save Yamamoto from Arachne, particularly when his pregnant wife Aya goes missing.

With the knowledge that Fueki is not only White Wizard, Koyomi's father, and the Phantoms' leader Wiseman, Haruto, Kosuke, and Mayu work together to try to discover his true plans.

With Gremlin in possession of the Philosopher's Stone, Koyomi dies. However, Fueki says that the light in Haruto's heart is the true Philosopher's Stone. Meanwhile, Gremlin, now evolved, goes on a rampage, and Kosuke cannot battle to save anyone or even himself from the monstrous Phantom.