Ten years after the Fourth Holy Grail War, the timid and insecure teenager Waver Velvet from Fate/Zero has grown up. He carries the heavy title of Lord El-Melloi II, the substitute head of the El-Melloi faction within the Mage's Association headquarters in London, known as the Clock Tower. Waver, once a student who stole his professor's artifact to prove his genius, now feels a deep responsibility for that professor's death. In response, the late professor's young heir, Reines El-Melloi Archisorte, essentially saddles him with the family's title and massive debts, forcing him to become the Lord of the Modern Magecraft Theory Department.

Despite his high status, Waver is a mediocre mage at best, holding only the rank of Fes. His true talent lies in his encyclopedic knowledge and his extraordinary ability to dissect and analyze any magical theory, which has earned him the ironic nickname "the destroyer of mystery". He chainsmokes cigars, is fascinated by video games, and is constantly stressed by his financial and political burdens. His main goal is to return to Fuyuki City for the Fifth Holy Grail War to summon his beloved King of Conquerors, Iskandar, once more.

Accompanying him everywhere is his quiet and loyal apprentice, Gray. A girl shrouded in a cloak, Gray is a former graveyard keeper from a rural village. Her face is identical to the legendary King Arthur, a side effect of her family's secret experiments to revive the king and the appearance of the real Saber in the Fourth Holy Grail War. She wields a powerful scythe-like lantern and possesses combat skills that far surpass her master, yet she is shy and hates attention. She is deeply devoted to Lord El-Melloi II, the first person who treated her like a normal girl.

Together, this unlikely detective duo investigates a series of magical mysteries plaguing the Clock Tower. The narrative is driven not just by "whodunit" but by "whydunit," focusing on the complex human and magical motivations behind the crimes.

The first major arc, case.剥离城阿德拉 (Adra Castle Separation), begins with Waver and Gray summoned to a remote castle to claim an inheritance. They are joined by other mages, including the affluent and talented Luviagelita Edelfelt. The late owner's will forces them into a brutal game of wits where failure means death, forcing Waver to use his intellect to survive.

Following this, case.双貌塔イゼルマ (Iselma) explores the elitist world of magecraft beauty and artifice. Waver is hired as a bodyguard for the next head of a family that creates "perfect" bodies, only to be caught in a locked-room murder mystery. Later, the long arc case.魔眼蒐集列車 (Rail Zeppelin) forms a major climax. Waver boards a train known as the Rail Zeppelin, an auction house for magical eyes. There, he confronts remnants of his past, including a Faker pretending to be Iskandar, and faces his own limitations as a magus, ultimately deciding to let go of his obsession with the Holy Grail War to protect his present family.

Throughout these arcs, the story delves into the dysfunctional politics of the Clock Tower. Waver's classroom is filled with brilliant but problematic students like Flat Escardos, a magical prodigy who is impossible to teach, and Svin Glascheit, a beast-like youth with an overly sensitive nose. These outcasts and misfits become his greatest strength, fiercely loyal to him as a teacher rather than the corrupt nobility he represents. The series serves as a bridge connecting the world of Fate/Zero to Fate/stay night, featuring cameos from characters like Kairi Sisigou, Olga Marie Animusphere, and even a young Rin Tohsaka. It is a story about guilt, legacy, and finding a place to belong in a world ruled by bloodlines and ancient mysteries.