"Kanojo ga Flag o Oraretara" centers on Sōta Hatate, a high school student who possesses the unusual 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, conflict, or even death. Sōta's life takes a dramatic turn when he transfers to Hatagaya Academy, where he encounters a diverse group of characters, each with their own unique flags and intertwined destinies.

The narrative unfolds as Sōta becomes entangled in the lives of several female classmates, including the cheerful and energetic Akane, the stoic and mysterious Nanami, the kind and nurturing Ruri, and the enigmatic transfer student Megumu. Each character's flags reveal complex backstories and hidden connections, often tied to Sōta's own past. As Sōta navigates these relationships, he discovers that his ability is linked to a larger, mysterious phenomenon involving the concept of "world lines" and the potential collapse of reality.

The story blends elements of romance, comedy, and science fiction, with a focus on the interplay between fate and free will. Sōta's interactions with the characters often lead to unexpected developments, as he attempts to alter their fates by "breaking" their flags. However, these actions sometimes result in unintended consequences, further complicating the narrative. The series explores themes of identity, memory, and the impact of choices on the future, all while maintaining a lighthearted tone through its comedic and romantic moments.

As the plot progresses, Sōta uncovers deeper layers of the mystery surrounding his ability and the true nature of the world he inhabits. The story builds toward a climactic resolution that ties together the various character arcs and the overarching conflict involving the stability of reality itself. Through its intricate plot and dynamic character interactions, "Kanojo ga Flag o Oraretara" presents a compelling exploration of destiny and human connection.