March 25th, 2095. To celebrate her 15th birthday, Miyuki Shiba goes shopping with her older brother Tatsuya in Yokohama. Miyuki enjoys her time with Tatsuya as if they are on a date, and she is ecstatic when he gives her a surprise gift. However, they are interrupted by a call from the main branch of their family, the Yotsubas, who are members of the Ten Master Clans. They ask Tatsuya to attend to an urgent matter. While Miyuki waits for Tatsuya to return, the fire alarm in the building goes off. Miyuki senses that this is a criminal act committed by someone using magic and heads toward the fire.

With the club recruitment week happening at First High School, Honoka and Shizuku, who are all-round outstanding students, are asked by various clubs to join. When they find themselves mobbed by club members, Eimi comes to the rescue, and the three of them become fast friends. One the way home from school, Honoka and her friends witness Tatsuya, who recently became a member of the Disciplinary Committee, being attacked by someone. Eimi, who is driven by her interest in this incident and in Tatsuya, decides to investigate who the attacker is. Honoka and Shizuku get pulled into Eimi’s investigation and the three girls end up forming the Girls’ Detective Club.

After observing the behavior of Mibu and the Kendo Club, Tatsuya concludes that the person who attacked him must be a member of the international anti-magic political organization, Blanche. Miyuki is infuriated by Blanche’s attempt to further the rift between Course 1 and 2 students. Meanwhile, Honoka and the Girls’ Detective Club identify the attacker as Kinoe Tsukasa, the captain of the Kendo Club. They begin pursuing him but find themselves surrounded by a mysterious bike gang. They try to use magic to retaliate, but are pushed into a tight spot when the attackers use Cast Jamming to nullify their spells.

During the public debate with the volunteer coalition, Blanche’s combat unit invades First High. Honoka and Shizuku almost get attacked but they fight back with magic. Thanks to Miyuki and her friends, the situation does not escalate out of control, but Honoka and the others are enraged with Blanche’s actions. Miyuki and Tatsuya head to the enemy hideout along with Erika in order to crush Blanche. When Blanche’s combatants ridicule magicians as being monsters, Miyuki unleashes her powerful magic on them.

First High is aiming to win for the third year in a row at the National Magic High School Goodwill Tournament of Magic Skills, also known as the Nine Schools Competition. Mayumi and the other seniors at First High are known as the most powerful team of their generation, and they are fired up about claiming victory again. However, Airi Isshiki, Shiori Kanou, and Toko Tsukushiin from Third High are determined to stop their winning streak. First High steadily stacks up points in the Nine Schools Competition, but during the Battle Board race, Mari, who was favored to win, is seriously injured in an accident. Mari, who desperately wants First High to take the overall victory in the tournament, asks Miyuki to take Mari’s place in the Mirage Bat event.

The Nine Schools Competition begins, and Shizuku goes head-to-head with Shiori in the Speed Shooting tournament. Shiori utilizes the “Arithmetic Chain” magic sequence which allows her to perform mathematical calculations faster than a supercomputer. Shiori left her own broken family to join Airi’s team, and her determination to win drives Shizuku into a corner. Honoka and her friends nervously watch the match, but Miyuki says, “Who do you think Shizuku’s engineer is?” with a confident smile. Just as she has predicted, Tatsuya has a secret tactic up his sleeve to bring victory to Shizuku.

On day two of the Rookie Events, Airi lives up to her epitaph, Éclair (Lightning), by using lightning-fast movement spells to dominate the Crowd Ball competition. Shiori is back in full force and crushes her opponent in Ice Pillars Break. While Third High steadily closes the gap with First High on the scoreboard, Miyuki makes her debut in the Ice Pillars Break tournament. The audience and the rival schools are blown away by her mind-boggling magical powers. Even Eimi is overwhelmed by Miyuki’s powers, but she must prepare to face Shiori in her next Ice Pillars Break match.

The match between Eimi and Shiori begins, with Eimi using the same tactics as in the qualifying rounds to destroy Shiori’s ice pillars so that First High can dominate the rankings. However, Shiori came prepared, and Eimi is driven into a corner. Meanwhile, Honoka takes on Touko in the Battle Board final. As a Light Element, Honoka uses her Light Magic and her ability to perceive light with her eyes and dodge the Ancient Magic traps laid by Touko. Touko takes the lead in the race, but Honoka still has some tricks up her sleeve.

The moment of Miyuki and Shizuku’s match approaches. Shizuku, who was hoping for a match against an excellent magician like Miyuki, heads into the match having seriously devised a plan with Tatsuya in order to win. Miyuki, who knows of Shizuku’s resolution, decides to challenge her with all her might. The Ice Pillars Break Final begins with a huge crowd watching on. Shizuku attacks with her strong vibration magic, but it fails to reach Miyuki’s pillars. When everyone believes it to already be over, Shizuku finally puts her secret plan into action. This technique even surprises Miyuki.

Replacing the injured Morisaki Shun and company, Tatsuya, Leo and Mikihiko will participate in the newcomers matches of Monolith Code. Miyuki, is anxious that the sabotage will reach Tatsuya and the others. Thereupon, Honoka and the first-year girls unite for the sake of Tatsuya in repayment for his assistance in the newcomers matches. Checking the Monolith Code stages and observing the venue, all to guard Tatsuya and the others. The matches proceed without incident as a result of the actions taken by Miyuki and the others, but there is another person who has noticed the abnormality of the stage.

It’s the day of the Mirage Bat Official Competition. Miyuki braces her hear for putting her all into winning the competition. On the other hand, Airi, frustrated with the power struggles between the Master Clans, swears to take the one-two finish with Mizuo Saho. Alongside this, Kobayakawa Keiko also encounters another accident during her match. Tatsuya sees through their trick with the CAD, so Miyuki is unaffected, but Miyuki is now First High’s only remaining player. Unable to lose the match, and not wanting to lose the match, Miyuki requests that Tatsuya permit the use of a certain magic.

Mirage Bat Official Competition Final. All the players are using Flying Magic, but amongst them only Miyuki, is racking up points. The other players, unfamiliar with Flying Magic, are forced to withdraw in quick succession, only Airi does not give up. Improvised Flying Magic and the High Speed and Jump magics that are her strong points, all so she can wield all her strength in this battle against Miyuki. Miyuki is surprised by her gallant form, whilst simultaneously strengthening her thoughts that ‘she cannot lose’. Miyuki vs Airi, clash between all their power. And as was expected, the winner is——!?

Honoka Mitsui and Shizuku Kitayama are accepted into First High. Ever since Honoka caught a glimpse of Miyuki at the entrance exams, she felt a strong admiration for her, and is overjoyed when they unexpectedly become friends. Honoka also respects Tatsuya for being an exceptional magician but is surprised to find out that he is a Course 2 student. She begins to wonder what the difference between Course 1 and 2 students are. When Honoka and her friends find themselves caught in a quarrel between Course 1 and 2 students, she tries to use magic to quell the dispute, knowing full well that it is against school rules to do so…