On the Old Islands (where the first game, The Legend of Dark Witch, takes place), humans and Fae are locked in combat. The Magic Lion Corps, an elite group of magic-wielding humans, poses a significant threat to the Fae. That is, until a sudden betrayal forces Magic Lion Corps member Day to be exiled from the Old Islands and ultimately results in the group being disbanded.

Day, bent on revenge, returns to the Old Islands. Her intentions are noted by Zizou Olympia, who descends upon Folkstone to stop her. Zizou's encounter with Day initially seems routine, but takes a sudden turn when Day activates "Capacity Zero" to drain Zizou of her powers. It is then that Zizou's sister Mati Olympia enters the fray and uses her powers to nullify Capacity Zero, resulting in Day's retreat.

Looking to gain more knowledge of the situation, Zizou seeks out the former members of the Magic Lion Corps: a familiar treasure fighter, a cynical shut-in, the newest librarian of Heavens Gardens, a motor-mouthed flower decorator, a mechanic currently working on a clock tower, a crafts director disguising herself as a Fae, a chivalrous thief, and a girl who fancies herself as a super hero. After defeating them, she then looks toward the Fae, and encounters a small witch with a big attitude, a strong but ditzy feline woman, a seductive woman with a pet snake, and a draconic soldier with a strong sense of honor.

The ending heavily depends on which character you play as. As Zizou battles the Fae, Day sets Folkstone on fire, leading to a face-off between the two in that area