One day, Yachi Haruaki receives a big black cube from his father, who works overseas. Overnight, the cube morphs into Fear, a tsundere loli who has turned up to remove the curse placed on her through accumulating negative emotions. At night, Haruaki encounters her stealing rice crackers, and allows her to stay at his place, much to the horror of Konoha, Haruaki's childhood friend.

Haruaki arranges for Fear to join his school, where to his surprise, she ends up well-liked and happy. After her first day, she goes home with Haruaki and Konoha only to be attacked by a strange woman trying to kill the "Fear in Cube".

Using her power to the full to beat Peavey, Fear calls up various torture devices using her cube to attack her, including a massive guillotine that cuts off her left arm completely. Still in a crazed state, Fear attacks Haruaki before running away and trying to commit suicide, but Haruaki goes after her.

Haruaki and Fear are faced with a life-and-death decision when Mummymaker pays them a visit.

The final battle between the maniacal Worse Hunter Peavey Barowoi and Fear happens just as Yachi and Konoha are sidelined! Making matters worse, Kirika is a defenseless hostage... or is she?

After returning to school, Fear and Haruaki are contacted by the principal once again, who tells them that a certain student, Shiraho hasn’t been turning up. Coincidentally, Shiraho was recently sent a box containing a cursed tool, and the doll, Sovereignty escapes by assuming human form. Haruaki and Fear try to track the doll down.

Haruaki, Fear, Konoha and Kirika find some inconsistencies in Shiraho’s story, so they go to check her out in the school records. When they see a picture of Sovereignty instead, they realize that the identities of the two girls aren’t exactly who they assume them to be.

Fear, Konoha and Kirika lure Sovereignty out by threatening to kill Shiraho, and Haruaki is forced to go along with their plan. After managing to call out all parts of the Killing Organ curse, Haruaki dispels the curse and Sovereignty and Shiraho are able to finally embrace. Everyone returns to school and Shiraho becomes a normal student again, with Sovereignty working in the principal’s office in a maid outfit.

Kuroe, an old friend of Haruaki’s and also a former cursed tool, returns to town and sets up her previously closed beauty shop, attracting many customers on its reopening date. At the same time, a new enemy makes herself known to the group – Alice, a weird woman who wants Fear to join her cause.

Fear, Konoha and Haruaki hear about a series of murders that have begun in town, realizing that the culprit is in fact Alice. Though they go to apprehend her, she easily escapes and hints that the girls she is murdering all have something in common. Fear arrives at Kuroe’s hair salon just in time to realize that she may be related to the murders, while Haruaki witnesses Kirika’s self-torture brought by the Kurokawa Karen.

The group begin their battle with Alice, only to find out that Alice’s magic mirror allows her to make solid duplicates of herself that last for 10 minutes, proven when Fear impales one of them through with a drill and has to watch as the clone gets torn up. The situation is pretty much hopeless…until Shiraho and Sovereignty turn up, releasing Kuroe from her body paralysis and breaking the mirror. Kuroe restrains the clones, allowing Haruaki and Fear to beat Alice. Before they can deal the final blow though, she jumps off a cliff and is rescued by a ship, saying that she’ll return to capture Fear someday.