At First High School, also known as Magic High School, the student body is rigidly divided by magical aptitude. The Course 1 students, or "Blooms," are the elite, while the Course 2 students, or "Weeds," are considered inferior. Tatsuya Shiba is a Weed with poor practical magic skills, yet he possesses an unparalleled talent for technical magic theory, analysis, and construction. His sister, Miyuki Shiba, is a prodigious Bloom, powerful and refined. The two are inseparable, bound by a deep loyalty that masks a more complex and secretive past.

Yoru no Tobari ni Yami wa Hirameku, or "Darkness Flashes in the Veil of Night," is a narrative arc that diverges from the main timeline, focusing on the shadows cast by the school's daylight hierarchies. The story begins when a series of bizarre, unsanctioned magical incidents occur after sundown, targeting students from both courses. These attacks are not random; they are precise and leave behind a faint, unique magical signature that only a few can detect.

The central conflict emerges as Tatsuya, operating as an undercover agent for the military's secret magic development division, is assigned to investigate these nocturnal disturbances. He is partnered with Miyuki, whose own abilities as a "humanoid" magical weapon make her both an asset and a liability. Their investigation leads them away from the classrooms and into the underworld of the city, where rogue magicians and black-market magic dealers operate. They cross paths with a mysterious figure known as the "Night Weaver," a magician who can manipulate magical energy into volatile, physical threads. The Night Weaver is not merely a criminal but seems to have a personal vendetta against the Four Great Magician Families and the entire educational system that produced them.

The setting shifts from the pristine, high-tech campus to the decaying industrial districts and illicit magic labs that thrive after dark. The narrative deepens when Tatsuya discovers that the Night Weaver is using an ancient, forbidden magical artifact to amplify their power, creating an "echo field" that allows them to attack multiple locations simultaneously. This forces Tatsuya to rely not on his flashy, combat-oriented sister, but on his own despised "decomposition" magic, which can dismantle any magical structure, to trace the artifact's origin.

As the arc progresses, Tatsuya is forced to confront the fact that the Night Weaver might have been a former Course 2 student driven to extremism after being used in an illegal magical experiment by a rival family. This revelation puts him at odds with the school's administration and even his own military handlers, who want to capture the Night Weaver for their own purposes. Miyuki, meanwhile, must grapple with her own protective and possessive instincts as she sees Tatsuya's secret life and the danger it attracts. A major narrative beat is a climactic confrontation in a flooded underground reservoir, where Tatsuya's decomposition magic and Miyuki's freezing abilities must combine in a synchronized, non-standard spell to counteract the Night Weaver's chaotic thread magic, a feat that threatens to expose Tatsuya's true power to the entire magic community.

The storyline weaves a tale of conspiracy and class resentment, where the bright, orderly world of the school is merely a facade for a far more dangerous, hidden magical war. Tatsuya’s primary objective shifts from a simple investigation to neutralizing the artifact and protecting the secret of his own existence, while Miyuki must choose between following orders and protecting her brother at all costs. The arc concludes with a tenuous victory where the artifact is destroyed, but the Night Weaver escapes, leaving behind a lingering threat and proof that the discrimination within the magical world breeds a darkness that no amount of academic ranking can suppress.