Two months after the tragic events of Corpse Party: Book of Shadows, Ayumi Shinozaki had paid the price for her use of black magic and been afflicted with a serious illness. However, she managed to somehow survive with the help of Naomi Nakashima. The grim grimoire, known as the Book of Shadows, now has laid waste to the Shinozaki estate and both the estate and tome vanished, leaving only a plot of land where it once stood.

Before she was hospitalized, one woman had appeared before Ayumi. This woman was Ayumi's older sister, Hinoe Shinozaki, who belongs to the W.I., the Wiccan Institute, an organization that worshiped spirits. There she listened to Hinoe's words...

"Regain the dark tome known as the Book of Shadows. For generations, the Shinozaki family protected that forbidden book and made it taboo to take it off the premises. In the wrong hands, this book will sink the world into the abyss and throw us all into the brink of chaos."

Ayumi's trail now leads into the once residence of Makina Shinozaki. She decided that it would be best to trust Hinoe's natural ability to sense calamity.

After being discharged from the hospital, Ayumi returned to Kisaragi Academy where Satoshi Mochida and friends gave her a warm welcome. However, the absence of Mayu Suzumoto and Yui Shishido were a constant reminder of their inevitable reality. Now a new, unfamiliar teacher's assistant supervises her homeroom. Then later, on her way home, a man approached Ayumi and told her, "If you reclaim the Book of Shadows and use it at Heavenly Host, those who have died there will be revived." The suspicious man's last words especially stuck in Ayumi's mind, "Those who have died there will be revived." Hinoe's and this strange man's words made Ayumi pledge that she will once more take back the Book of Shadows.

The following day, Ayumi went to visit the estate where Makina Shinozaki resided. However, it was run-down and looked to have been closed for a long time; "NO TRESPASSING" tape was strewn up everywhere, blocking entry.

She stared intently at the estate with fierce determination. ...She couldn't afford to let Satoshi and the others be involved this time.

For Ayumi, it was the responsibility of Shinozaki's bloodline. The lone struggle and legacy of her lineage.