News outlets were enthusiastically reporting the great success of the stellar furnace experiment carried out by the students at First High School. However, since Takuma Shippou had heard from his father that the Saegusa Family was going to be the ones to deal with Diet member Kanda, he thinks they used Tatsuya to claim credit for the experiment's success themselves. Takuma then takes his pent-up anger out on Kasumi Saegusa, who he happened to pass by on campus. Kasumi, unable to turn a blind eye to these insults against her family, is on the brink of engaging in a magic fight with Takuma... But then, the Disciplinary Committee intervenes before either of them makes their move, and takes them in for questioning. Tatsuya suggests they let them duke it out in an official match to end this mutual enmity between the two once and for all.

The women's division of the Steeplechase Cross-country Event has finally begun. Tatsuya has Pixie figure out the location of all the parasite dolls and tries to eliminate them before they come into contact with the players. However, the parasite dolls unleash their magic at speeds that exceed Tatsuya's imagination. Though it is difficult, he manages to seal away the first parasite doll. Tatsuya goes on to seal away the remaining parasite dolls one after another, but the highest-performance models, the Prime Four, now stand in his way.

Tatsuya and the other Student Council members were spending their days extremely busy in order to deal with the sudden change of events for the Nine Schools Competition. However, out of the blue, Tatsuya receives an email from an unknown sender. The email states that the changes in the competition were due to pressure from the JDF, and that the Kudou Family was planning to piggyback on the JDF's order to test out a secretly developed military weapon at the Steeplechase Cross-country Event. This prompts Tatsuya to head to Nara, where the Kudou Family's stronghold is based, to find out more about the experiments they are conducting.

In order to obtain cooperation from Retsu Kudou to capture Gongjin Zhou, Tatsuya, Miyuki and Minami visit Nara, the home of the Kudou Family. Retsu Kudou readily accepts Tatsuya's offer and introduces him to his grandson, Minoru. Minoru is one year Tatsuya's junior, and although he is physically weak, he is said to be a very powerful magician. At the dinner table, Minoru hears that Tatsuya and his friends are looking for a traditional magic user and offers his help. The next day, as Tatsuya and the others are scouting the Traditionalists' base in Nara under Minoru's guidance, they are attacked by the Traditionalists at Nara Park.

Colonel Balance orders Lina to capture the caster who was behind Scorched Halloween. Balance gives Lina a custom-made device called "the Brionac" which converts Strategic-Class magic into a beam of high-energy plasma.

The Nine Schools Competition has ended, and it is now the second semester. Ayako and Fumiya visit Tatsuya to deliver a letter they were entrusted directly from Maya. The letter was a request asking for Tatsuya's cooperation in capturing Gongjin Zhou. The Kurobas were also pursuing him but lost sight of him in the Kyoto area. It seems Gongjin Zhou has been receiving help from the Traditionalists, a faction of Ancient Magicians, in his escape. The Traditionalists and the Kudou Family have been in conflict with each other for many years. So, Tatsuya decides to reach out to Fujibayashi, Retsu Kudou's granddaughter, to ask for Retsu's cooperation in capturing Gongjin Zhou.

Finally, the day has arrived for Monolith Code. Tatsuya and his teammates have a strategy against Cardinal George and the Crimson Prince. Miyuki is confident that her brother will be the winner. However, is there a bad surprise in store for First High?

It turns out that the masked magician that engaged in a sword fight with Erika was Lina. With her identity blown, Lina uses the Parade spell to attack Tatsuya. Tatsuya attempts to disable the Parade spell by dismantling it but fails.

The nationwide Magic High Schools Thesis Competition held by the Japan Magic Association. Also known as just The Thesis Competition will be held in Kyoto. After experiencing the Thesis Competition being attacked by the Great Asian Alliance last year, Mikihiko, the head of the Disciplinary Committee, proposes to the Student Council that this year they would like to inspect the area around the venue in advance to ensure security. Tatsuya, Miyuki, Minami, Leo and Erika will also be accompanying him. On his way home after the Student Council meeting, Tatsuya learns from the news that Mayumi's bodyguard, Saburo Nakura, was murdered by someone in Kyoto.

First High School students celebrate their victories in the Nine Schools Competition. Enraged by the actions of No-Head Dragon, Tatsuya pays them a visit. Since Tatsuya is not a member of the Ten Master Clans, Jumonji has a very interesting offer for him.

After terrorists attack the Thesis Competition, the students have to fight to survive.

The battle rages on after the attack on the Yokohama Convention Center. Students fight to make it safely to the shelter while forces duke it on the streets.

Miyuki reveals the price her brother has to pay in order to use his extraordinary power. Tatsuya, meanwhile, makes use of a destructive weapon. All battles come to a head.

Information gets out that Kanda, an anti-magic advocate and Diet member, will visit First High School with the media to observe the school's curriculum, claiming that he has heard disturbing rumors about it. He plans to create an uproar with the media and assert that the school is brainwashing students into the military - if he finds anything suspicious of that nature. To stop this ploy, Tatsuya suggests performing an experiment showing the students creating a Sustained Gravity Control-Type Magic Thermonuclear Fusion Reactor = Stellar Furnace. The students plan on demonstrating that the magic education they receive at the school can solve energy problems, and that magic can contribute to the peace of humankind depending on the type of magic they use.

A notice has been sent to the magic high schools across the country that a portion of the events in the Nine Schools Competition will be changed. Shockingly, three of the six events will be changed. In order to respond to the sudden change in events, First High School's Student Council is thrown in a frenzy to understand the new rules, reselecting athletes and readjusting their CADs. While everyone was complaining about the Competition's management due to the sudden change in timing, one month before the start of the Nine Schools Competition, Tatsuya had a growing suspicion about the strong military flavor of all the newly added events.

It turns out that the secret experiments that the Kudou Family has been conducting was for developing parasite dolls, a female combat robot possessed by a parasite. Experiments on the dolls' operations are being conducted at the Steeplechase Cross-country venue, where security is abnormally tight - so much so that Tatsuya himself can't even break into the premises. As such, Tatsuya orders Pixie to keep an eye out for the parasites while he conducts adjustments to the CADs and gives instructions to the underclassmen as an engineer. However, this continual sense of nervousness and nonstop days of hard work are tiring out Tatsuya. He's never felt this tired before.

The night before the Thesis Competition. Tatsuya receives a report from Fumiya that they have located Gongjin Zhou's whereabouts. He was hiding at the JGDF's 2nd Supply Base in Uji. Tatsuya speculates that he would not have enough offensive power to fight alone at the JGDF's base, so he contacts Masaki. When Masaki hears that they would need to invade an army base to get to him, he hesitates for a moment but decides to accompany Tatsuya to fulfill his responsibilities as a member of the Ten Master Clans. The two invade the army base where soldiers controlled by Gongji Zhou await...

Tatsuya meets Masaki Ichijo and Shinkuro Kichijoji. It takes them by surprise that Tatsuya already knows about their background. Another accident happens at the Nine Schools Competition. First High students think that it was another act of sabotage.

Tatsuya is asked to compete in Monolith Code. He picks Leonhard and Mikihiko to be his team members. Kichijoji advises Ichijo to figure out a way to force Tatsuya into head-to-head combat to win Monolith Code. Will Tatsuya take the bait as expected?

Tatsuya has brought the Relic to FLT. The lab is hacked by the Great Asian Alliance. An insider attempts to go through the personal belongings of Tatsuya at the Robot Research Club. Will the Relic be safe?

As instructed by Raymond, one of the Seven Sages, Tatsuya and his friends head to the outdoor training area behind First High School on the night of February 19th. Just as Raymond said, they detect the presence of all active parasites and Lina gathering at the scene. At this rate, clashing with Lina, who is hell-bent on completing her mission as Sirius, will be inevitable. With complex emotions at play, the final battle with the parasites begins.

It has reached the month of April in 2096, and various aspects of Tatsuya's life was changing as he advances to the second year. Tatsuya and Mizuki transferred to the newly established Department of Magical Engineering, and Mikihiko has also transferred out of Course 2, and was now a Course 1 student. Along with this change, Tatsuya and Miyuki were now living with Minami who was sent to stay with them by the Yotsuba Family. Tatsuya enters the school year hoping they would have a peaceful student life this time around, but the new year meant the arrival of new students, like Kasumi and Izumi, the twins of the Sagusa Family, and Takuma Shippou, the new student valedictorian who feels a rivalry towards the Saegusa Family. All of them having their own quirk or two, for better or for worse...

Tatsuya and Miyuki visit FLT where a Flying Spell experiment is taking place. They run into members of the Yotsuba family there. Tatsuya sees Mikihiko practicing Spirit Magic. Since Tatsuya seems to be interested, Mikihiko tells him about Crystal Eyes.

Tatsuya's computer is hacked. He starts investigating the identity of the attackers and suspects that it has to do with the upcoming Thesis Competition. First High students sense that they are being watched. Will they be able to find out what is going on?

A parasite is an information body that was generated from the spirit dimension. How could an entity from another dimension appear in the physical world? An evil visitor of unknown origin infiltrates its way into First High School.