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.

Following the events of "Scorched Halloween," the UNSA dispatches the most powerful asset in its arsenal to Japan to uncover the identity of this person—the elite magician unit "Stars". Meanewhile, Tatsuya and his friends are having a farewell party for Shizuku, who is leaving to study abroad. Around the same time, Tatsuya is informed about the USNA's plan to uncover his true identity. Elsewhere in Tokyo, numerous reports arise of seemingly random bodies found drained of blood. It does not take long for Tatsuya to realize that it is not a mere coincidence.