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Haruhi Kamisaka is one of the mages in training at Mizuhosaka Academy who on Valentine's Day, runs into Yūma Kohinata, who she believes may be a boy she's been trying to find for years. After the magic section of the academy suffers from a gas explosion, Haruhi and her friends transfer over to the normal section and Haruhi ends up in Yūma's class.

A new school year has begun and the upperclassmen prepare for the entrance ceremony. Of the new students, Sumomo, Yūma's sister, is entering as a first year student. Later, Haruhi and Anri are invited by Yūma and his friends to participate in the cherry blossom viewing with them occurring the following Sunday.

The students aren't coming to the school cafeteria as often as they used to and Anri begins working as a waitress in order to bring in business. However, complications arise.

Tama-chan, Koyuki's magical wand, starts to feel that he's not very important compared to the other thousand similar Tama-chan's Koyuki has made. Tama-chan leaves Koyuki for a time because he is in doubt of her feelings towards the Tama-chans she has made.

Hachisuke thinks he has found a beautiful female ghost at school and promises to "send her to heaven." Upon revealing this knowledge to his friends, they all go with him to school at night to find out if what he saw really was a ghost and if there's anything they can do about it.

A new female student named Ibuki Shikimori transfers into Sumomo's class, though is cold towards everyone and thus has no friends. Sumomo, feeling bad for her, tries very hard to become her friend.

In an attempt to make Ibuki more friendlier towards others, Haruhi and her friends think up ways that they can spend time together with Ibuki, such as eating lunch together, playing games together, or going out bowling together. At the end of the day, Ibuki starts to view the others as friends.

Yūma and his friends get the chance to go to the school's practice area away in the mountains, but they are just using it for a light vacation during the summer. While there, Yūma and Haruhi become closer and start addressing each other by their given names.

The school festival has arrived, and all the students are getting prepared. Near the end of the festival, Ibuki takes Yūma captive, and attempts to force Haruhi to give up the secret to break the barrier on Shikimori Forest.

Sumomo has been affected by a spell from the fight between Haruhi and Ibuki at the school festival, and is unconscious. Yuma's past is revealed to Haruhi and Anri along with a related event that caused the death of Ibuki's older sister.

Yūma's biological mother starts to help Sumomo's condition, but in the meantime Ibuki goes within the barrier in Shikimori Forest to obtain the Shikimori Treasure. Meanwhile, Jun takes Yūma to the aquarium to cheer him up, but Yūma leaves when Jun is not looking.

Demons appear in the forest and the mages try to stop them. Yūma's power is needed to stop the Shikomori Treasure, the source of the demons, but he firmly believes that magic only brings unhappiness. Haruhi tells Yūma that she was the girl saved by his magic in the past, and that magic can also be a source of happiness if used correctly. Haruhi then proceeds to kiss Yūma. Afterwards, Yūma uses the flute and seals the monsters away once more. In the end, Yūma transfers to the magic section and is now together with Haruhi.