"Kanojo ga Flag o Oraretara" centers on Sōta Hatate, a high school student who possesses the unique ability to see "flags" above people's heads, which indicate their future actions or emotional states. These flags can signify various outcomes, such as friendship, romance, or even death. Sōta uses this ability to navigate social interactions, often trying to prevent negative outcomes by "cutting" these flags. His life takes a dramatic turn when he transfers to Hatagaya Academy, a prestigious school with a mysterious past tied to his own family.

At the academy, Sōta encounters a diverse group of characters, each with their own complex flags and backstories. Among them is Nanami Knight Bladefield, a half-Japanese, half-British girl who claims to be his fiancée, and Akane Mahōgasawa, a cheerful and energetic classmate who quickly becomes close to him. Other key characters include Rin Eiyūji, a stoic and skilled swordswoman, and Megumu Tōzokuyama, a mischievous and cunning girl with her own hidden agenda. As Sōta interacts with these individuals, he uncovers deeper mysteries surrounding the academy, his family, and the true nature of his flag-seeing ability.

The narrative blends elements of comedy, romance, and supernatural intrigue, with Sōta often finding himself in absurd or dramatic situations as he tries to manage the flags of those around him. The story gradually reveals that the academy is connected to a larger, more sinister plot involving parallel worlds, ancient prophecies, and the concept of "world lines"—alternate realities that intersect and influence one another. Sōta's ability to see and manipulate flags becomes crucial in navigating these overlapping realities and preventing catastrophic events.

As the series progresses, the relationships between the characters deepen, with romantic tensions and personal conflicts adding layers to the story. Sōta's interactions with the female leads, particularly Nanami and Akane, drive much of the emotional core of the narrative. The series also explores themes of fate, free will, and the consequences of one's choices, as Sōta grapples with the moral implications of altering others' destinies through his ability.

The plot takes unexpected turns, incorporating elements of science fiction and fantasy, as the characters uncover the truth about the academy's origins and their own roles in the unfolding events. The story builds toward a climactic confrontation that ties together the various threads of the narrative, resolving key mysteries while leaving room for emotional and thematic exploration. "Kanojo ga Flag o Oraretara" combines lighthearted moments with dramatic stakes, creating a multifaceted story that appeals to fans of multiple genres.