One summer's day, Nanase Takeshi sees Aiba Mui, a girl in a school uniform he's never seen before, collapse outside the kendo clubroom at his school. Takeshi carries the unconscious Mui to the Nurse's Office to get her medical help, but upon waking, Mui takes him for a suspicious character with less-than-pure motives.

After encountering Mui, a girl magician, Takeshi, Kurumi and Ida have also been turned into magicians. As a result, they have also become targets of the Ghost Trailers, the antagonistic magician gang that had erased Mui's older brother's memories in order to control him.

Takeshi and his friends have enrolled at Subaru Magic Academy in order to start learning magic. One day during class, Mui receives tickets to see a fortune-teller from Violet-sensei, the English teacher, and invites Kurumi to go with her.

Takeshi and Ida are at an early-morning practice session trying to master control of their magic. When Kurumi finally arrives, it is with the news that Mui did not return to the girls' dorm the previous night. From the looks of a map they discover on her desk, it seems Mui has again gone off to try to get back her older brother Tsuganashi.

Based on their performance during the school-wide Ancestral Magic exam, Takeshi and friends may be allowed to participate in the operation to recover Mui's brother Tsuganashi. The exam is split into separate levels where each of the different types of Ancestral Magic is tested separately.

Based on their superior performance during the Ancestral Magic exam, Takeshi and his friends are allowed to participate in the operation to recover Tsuganashi as they were promised. The School Director, Momoka, takes them with her to battle, where she faces Washizu while Takeshi's group faces Tsuganashi. However, Mui's indomitable desire to save her brother at any cost causes her to take extreme actions...

It's now April, and Subaru Magic Academy bustles with activity welcoming its new students. Among them are Ida's younger sister Futaba. Due to an unfortunate little incident between the Ida siblings, Futaba has become a magician as well. Also among the new students is Takeshi's younger brother Gekkou.

Ryuusenji Kazuma, the leader of the Ghost Trailers, had fallen into endless slumber after the previous Great War. Now that he has awoken once again, the curtain rises upon the Second Great Magic War.

After revealing that he is a Ghost Trailer, Gekkou takes Kurumi and Twilight away from Takeshi. The badly wounded Takeshi is rescued by Kisaki Ena and her companions from the Community known as "Camelot."

Takeshi continues training at Camelot in order to rescue Kurumi. Meanwhile, at the Ghost Trailers' headquarters, Kurumi confronts Gekkou. Taking advantage of a moment's carelessness, Kurumi manages to escape her prison.

Having finished his special training at Camelot, Takeshi returns home to find Gekkou emerging from their house with Twilight gripped in his right hand—dripping with blood. The nightmarish vision Takeshi had once seen through Twilight's power has finally come to pass. Gekkou claims that he struck down their mother in self-defense. Unable to suppress his rage at seeing his loved ones hurt any longer, Takeshi finally finds the heart to battle Gekkou decisively.