Gu Jie, a magician who orchestrated a sinister suicide bombing by manipulating corpses to do his bidding, has gone into hiding somewhere in Japan. As public outcry against magicians builds and humanist forces gain momentum, the Ten Master Clans task Tatsuya, Katsuto, Mayumi, and Masaki with determining the whereabouts of the mastermind behind the bombings. But when Major Benjamin Canopus, the second-in-command of the most powerful magic unit in the United States, starts gunning for Gu Jie as well, Tatsuya becomes inexplicably enraged!

At the same that the leader of the USNA's elite magician unit, the Stars, traveled to Japan under the identity of an exchange student named Lina, the parasite incident wreaked havoc on the First Magic High School until Tatsuya and his friends saved the day and brought the incident to a peaceful conclusion. However, the parasite merely lost its first host and continues to wander this world. More importantly, it's found its next host-a humanoid helper robot. After copying Honoka Mitsui's behavior and patterns, the parasite has been reborn as Pixie, vowing to follow and serve Tatsuya. After learning more about parasites from Pixie, Tatsuya gathers Miyuki and the others to head towards the Aoyama Cemetery to fight against a new impending danger!

April 2096 has arrived. Despite the commotion they were involved in, Tatsuya and Miyuki safely passed all of their classes and are now returning as juniors for another semester. In light of Tatsuya’s accomplishments, a magic engineering curriculum has been established, granting him a new lease on proper student life. With his new classes and his position as acting student council vice president, Tatsuya is certain that this year for sure, he’ll be able to enjoy a peaceful time at school with his sister...until three freshmen form the elite Numbered families start raising hell in their First High debut!

December, 2095. In exchange for Shizuku going to study in the USNA, Lina has been attending Magic High School in Japan. Tatsuya figured out her true identity as a member of USNA special forces right away but as soon as one mystery is solved, another breaks out. Right around the same time as Lina's arrival in Japan, there has been a series of attacks on magicians by something called the "vampire." But while Tatsuya and Mikhiko try to use old magic to discover the identity of this criminal, an assault on their school occurs!

Spring is here, and the graduating seniors of First High are planning a getaway to sunny Okinawa. At the same time, Tatsuya and Miyuki will be on the island as the Yotsuba family’s representatives at a memorial service for the victims of the invasion there several years earlier. Of course, this is just a cover for their true purpose: foiling a terrorist plot hatched by some deserters and Australian operatives. Their primary target is a party that Shizuku and Honoka will be attending—What are the chances? Romance is in the air, and danger is on the horizon, making this a vacation they’ll never forget!

The Ten Master Clans and the Eighteen Support Clans have gathered for a conference to raise concerns about Tatsuya's behavior. His official position is that all his actions were necessary to protect Miyuki and he has the full support of the Yotsuba, including the current head of the clan, Maya. Naturally, some of the other families are not so easily convinced. And while this captures everyone’s attention, Mitsuya Shiina vanishes without a trace, kicking off yet another incident that may affect more than just First High...

March 2097—Brazil deploys the strategic-class spell Synchroliner Fusion in South America, starting a wave of unrest that will reach as far as Japan, where the new school year is just beginning. Tatsuya and Miyuki have entered their third year at First High, but anti-magician sentiment has been steadily rising. As many young scions of the twenty-eight families gather to discuss what to do about the concerning political climate, a much more immediate threat sits just beyond the shores of Sado Island...