Every day, Aya Asagiri thinks about killing herself. She is bullied relentlessly at school, and at home, her older brother Kaname physically abuses her to relieve the academic stress put on him by their father. One night, as she lies awake wishing for death, a mysterious website called Magical Girl Site appears on her laptop, promising to give her magical powers. At first, she dismisses it as a creepy prank, but when she finds a magical gun in her shoe locker the next day, she doesn't know what to believe. Deciding to take it with her, she soon runs into her bullies once again. But this time, desperate for anything to save her, she uses the gun—and her assailants are transported to a nearby railroad crossing, where they are run over. Aya's conscience is unable to handle the fact that she murdered two of her classmates with magic, and she desperately tries to understand the situation. However, when she finds herself in trouble again, she is saved by Tsuyuno Yatsumura, a classmate who can use magic to stop time. This duo has a lot to do: not only do they have to fight alongside and against other magical girls, but they also need to uncover the truth behind the website and the apocalyptic event known as The Tempest that is soon to occur.

Extra episode of Mahouka Koukou no Rettousei: Yoku Wakaru Mahouka! included in the BD/DVD.

In the story, the seasons have changed and it will soon be the second spring. Tatsuya and Miyuki have finished their first year at First Magic High School and are on their spring break. The two go to their villa on the Ogasawara Island archipelago. After only a small moment of peace a lone young woman named Kokoa appears before them. She has abandoned the Naval base and she tells Tatsuya her one wish. (Source: ANN)

In the dawn of the 21st century, magic, long thought to be folklore and fairy tales, has become a systematized technology and is taught as a technical skill. In First High School, the institution for magicians, students are segregated into two groups based on their entrance exam scores: Blooms, those who receive high scores, are assigned to the First Course, while Weeds are reserve students assigned to the Second Course. Mahouka Koukou no Rettousei follows the siblings, Tatsuya and Miyuki Shiba, who are enrolled in First High School. Upon taking the exam, the prodigious Miyuki is placed in the First Course, while Tatsuya is relegated to the Second Course. Though his practical test scores and status as a Weed show him to be magically inept, he possesses extraordinary technical knowledge, physical combat capabilities, and unique magic techniques—making Tatsuya the irregular at a magical high school.