The story of Mawata no Ori unfolds in a provincial Japanese city during the late Showa period, centering on the Himuro family, who operate a small but reputable confectionery shop. The narrative is driven by the strained and complex relationship between the protagonist, a young woman named Yuki Himuro, and her overbearing mother, Sumiko. Sumiko is a formidable matriarch who rules both her household and the family business with an iron will, enforcing a rigid code of conduct and appearance to maintain the shop's pristine public image. Yuki, in her late twenties, has spent her entire life subjugated to her mother's relentless expectations, working in the shop and enduring Sumiko's constant criticism and emotional manipulation, which has left her socially stunted and devoid of personal ambition.

The plot is set in motion when Yuki’s younger brother, Ryo, returns home from Tokyo with his wife, Miyako, and their young child. Ryo’s homecoming disrupts the fragile, stagnant equilibrium of the Himuro household. Unlike Yuki, Ryo escaped their mother’s dominion years ago, and his arrival forces a confrontation with the unspoken family dynamics. Sumiko’s favoritism toward Ryo becomes immediately apparent, yet she simultaneously resents his independence and his wife, whom she views as an interloper. Yuki, who has long accepted her role as the sacrificial daughter, begins to experience a painful awakening. She observes Miyako’s quiet defiance and Ryo’s attempts to set boundaries, which starkly contrasts with her own helplessness. A key narrative arc involves the deteriorating health of the family patriarch, Yuki’s father, who is a silent, passive figure. His illness serves as a catalyst, forcing the family to address the shop's succession and bringing to the surface long-buried resentments and secrets regarding Sumiko’s own past as a young bride who was similarly oppressed.

As tensions escalate, Yuki finds an unlikely confidant in a kind but awkward customer, a local salaryman named Takeda, who shows her genuine respect and kindness. This budding, tentative relationship represents Yuki’s first step toward self-discovery and rebellion. She begins to secretly take art classes, a hobby her mother had forbidden as frivolous, discovering a sense of self-worth outside her role as her mother’s assistant. This secret life becomes a source of both strength and immense guilt. Concurrently, Sumiko’s grip on the family tightens as she becomes paranoid about losing control, leading to increasingly cruel and manipulative acts, including sabotaging Yuki’s art supplies and attempting to drive a wedge between Yuki and Takeda. A pivotal arc sees Yuki finally confront her mother about a past incident—the arranged termination of a pregnancy Yuki was forced into as a young woman, a trauma that was buried and never discussed. This revelation shatters the unspoken rules of the household and forces every family member to choose a side.

The narrative builds towards a climax during the annual city festival, a significant event for the confectionery shop. Overwhelmed by her mother’s public praise of her while privately demeaning her efforts, Yuki suffers a breakdown and leaves the shop mid-event. This public act of defiance is a turning point. In the aftermath, the family fractures. Ryo decides to move his family back to Tokyo, permanently severing ties with his mother. The father passes away, leaving the shop and its legacy in limbo. The final arc of Mawata no Ori follows Yuki as she makes the painful decision to leave the household entirely, choosing a small, independent life over the suffocating security of the family business. She does not seek grand reconciliation; instead, she finds a quiet resolution in accepting her own desires, even if it means living in poverty and estrangement. The manga concludes not with a triumphant victory, but with Yuki in her modest apartment, a single piece of her own artwork on the wall, symbolizing her fragile but hard-won freedom from the oppressive cocoon, or the "cotton-wrapped prison," of her mother’s home.