"If Her Flag Breaks" centers on Sōta Hatate, a high school student with the unique ability to see "flags" above people's heads, which indicate significant events in their lives. These flags can signify anything from impending danger to romantic opportunities. Sōta uses this ability to help others, often intervening to change their fates. His life takes a dramatic turn when he transfers to Hatagaya Academy, where he encounters a diverse group of female characters, each with their own distinct personalities and backstories.

The narrative unfolds as Sōta becomes entangled in the lives of these girls, including the cheerful and energetic Nanami Knight Bladefield, the stoic and mysterious Akane Mahōgasawa, the kind and gentle Kikuno Shōkoji, and the mischievous and playful Rin Eiyūji. Each girl has her own set of challenges and "flags" that Sōta must navigate, often leading to comedic and heartfelt moments. The series blends elements of romance, comedy, and supernatural intrigue as Sōta's interactions with the girls deepen, revealing their individual struggles and aspirations.

As the story progresses, Sōta's ability to see and manipulate flags becomes increasingly complex, with the narrative exploring the consequences of his interventions. The series also delves into the concept of fate versus free will, as Sōta grapples with the ethical implications of altering others' destinies. The relationships between the characters evolve, with romantic tensions and friendships developing in unexpected ways.

The plot is driven by a mix of episodic encounters and overarching storylines, with each episode typically focusing on a specific character or situation. The series maintains a lighthearted tone, punctuated by moments of emotional depth and introspection. The interactions between Sōta and the girls are central to the narrative, with their dynamics providing both comedic relief and character development.

By the end of the series, the characters' arcs reach satisfying conclusions, with Sōta's role in their lives solidifying his place as a pivotal figure in their stories. The resolution ties together the various plot threads, offering closure to the central themes of fate, relationships, and personal growth. The series balances its supernatural premise with relatable human experiences, creating a narrative that is both engaging and accessible.