"Angel's 3Piece" centers around three sisters—Kotoha, Yuzu, and Aoi Takamura—who live in a strict Catholic boarding school, St. Michael's Girls' Academy. The school enforces rigid rules, prohibiting students from engaging in activities deemed inappropriate, such as listening to secular music or interacting with boys. Despite these restrictions, the sisters secretly form a rock band called "Angels," using their shared love for music as an escape from the oppressive environment.

Kotoha, the eldest sister, is the band's guitarist and vocalist, embodying a calm and responsible demeanor. Yuzu, the middle sister, plays the bass and is more rebellious and outspoken, often challenging the school's rules. Aoi, the youngest, is the drummer and is characterized by her shy and reserved nature. The band's existence is kept hidden from the school authorities, and the sisters perform in secret, often sneaking out to practice or perform in nearby locations.

The narrative explores the sisters' struggles to balance their passion for music with the strict expectations of their school and society. Their lives take a turn when they encounter a young priest-in-training, Shintaro Kurusu, who discovers their secret. Instead of reporting them, Shintaro becomes an ally, helping them navigate the challenges they face while keeping their band hidden. His involvement introduces themes of trust, rebellion, and the clash between personal freedom and institutional control.

As the story progresses, the sisters face increasing scrutiny from the school administration, leading to moments of tension and conflict. Their bond as sisters and bandmates is tested, but their shared love for music and determination to express themselves ultimately strengthens their resolve. The series delves into themes of individuality, familial loyalty, and the pursuit of passion in the face of adversity, all set against the backdrop of a restrictive and authoritarian environment.