Hundreds of years ago, invaders from the sky known as the Celestial Hosts nearly destroyed the world. Five legendary mages united to repel them, raising a powerful barrier atop a colossal tower named Mercedes Caulis. These five became the first Magia Vander, the highest rank of mages, and each generation's strongest successors must maintain the barrier from the tower.

Will Serfort is a sixth-year student at the Rigarden Magical Academy, a school dedicated to training future mages strong enough to become Magia Vander. He has made a promise to his childhood friend, Elfaria Albis Serfort, that he will climb to the top of Mercedes Caulis and reunite with her. The problem is that Elfaria has already achieved the rank of Magia Vander five years ago, becoming the youngest ever to do so, while Will cannot use any magic at all. He is regarded as a failure and ridiculed by classmates and instructors alike.

Will compensates for his complete lack of magical aptitude through relentless physical training and exceptional swordsmanship. He earns credits by hunting monsters in the school dungeon, where his combat skills allow him to defeat creatures that even skilled mages struggle against. He also consistently achieves perfect scores on written exams, but his inability to cast spells keeps him on the brink of expulsion.

The academy is governed by a magic-first hierarchy. Teachers like Edward Serfence actively try to force Will out, while a few, such as Workner Norgram, recognize his potential and support him. Will makes a handful of allies among his peers: Colette Loire, a kind healer who trusts him from the start; Sion Ulster, a proud lightning mage who starts as a rival; Julius Reinberg, a narcissistic noble with ice magic; Wignall Lindor, an elf illusionist; Lihanna Owenzaus, the top-ranked student with lightning magic; and Rosti Nauman, his supportive roommate whose secrets hint at a deeper role in the story. Will also acquires a small carbuncle familiar named Kiki, which can cast reflective magic.

The first major narrative arc revolves around the Grand Magic Festival, a tournament where the Magia Vander gather to scout talent. Will is forced to participate after a confrontation with Julius, and his battles begin to reveal the true extent of his swordsmanship to the academy. The festival culminates in a fight where Will's abilities start to shake the established order.

The second major arc is a mandatory dungeon expedition known as the Comprehensive Practical Training. The students are sabotaged by unknown assailants and thrown into deep, dangerous levels where a colossal monster called the Evil Grand Duke is summoned. Will and a small group of classmates must cooperate to survive. The incident results in casualties and introduces the presence of a mysterious group called the Book of Ruin, which has infiltrated the academy and the tower.

The third arc takes place during the Boundary Festival, an annual ritual where the Magia Vander renew the protective barrier. The Book of Ruin attacks the city, unleashing powerful monster from deep within the dungeon. Will's friends are gravely wounded, and Rosti loses an arm. In a moment of crisis, Will is guided by a mysterious boy named Finn and awakens a latent power: the ability to create a magical sword, or "Wis," by channeling the magic of others. He defeats the special monster, a Divende, and this act is recognized as the creation of new magic.

As a result, Will is allowed to graduate and ascend to Mercedes Caulis. However, life at the tower presents new challenges. The mages are divided into factions, and Will is unable to join any of them because he cannot independently load magic into his sword without relying on others. He is forced to train to master a technique called "Sōten" (imaginative loading) to generate his own magical swords. This leads him to recover lost memories from his childhood with Elfaria and uncover the truth about his own nature. The later arcs involve political intrigue within the tower, the murder of Julius Reinberg, and an escalating war between the Book of Ruin and the Magia Vander. Will and his allies from the Thunder faction descend into the dungeon on an expedition that puts them directly in the path of the enemy, eventually confronting the revived celestial invaders and the source of the original threat.