The story of FLAGS unfolds in an era dominated by the great Ouka Empire, which rules over one third of the world. To maintain peace and prevent rebellions among its territories and other nations, the empire hosts the Ouka Battle Competition once every eight years. In this tournament, five representatives called Patriots are sent from each country to compete. The victors are granted immense fame, honor, and fortune. The narrative follows Kurou Akazome, a boy from the peninsula of Taiyou in the kingdom of Toutou, who walks the same path as his father to become the strongest Patriot.

For eight years, Kurou has faithfully waved a large triple flag on a cliff each day, believing his father, Tsubame Akazome, is still alive and will return home after winning the tournament. His daily ritual has granted him extraordinary gripping strength in his hands and fingers. Kurou's world changes when a ship arrives carrying five individuals who introduce themselves as the Patriots of Toutou. One of them, Nishiki, was Tsubame's comrade in the previous tournament. He delivers the news of Tsubame's death in the competition and presents Kurou with his father's weapon, the Bansantou. The Bansantou is a simple iron bar with eight holes carved into it. Each hole, when activated by a member of the Akazome bloodline, transforms the bar into a different weapon form based on the user's imagination. Before Kurou can officially join the team for the upcoming tenth tournament, he must prove himself by activating the first hole within a single day.

Tsubame had made many enemies during his time, and a group of vengeful pirates he once defeated, the Alliance of Eastern Russia Sea Pirates, attacks Kurou's hometown seeking retribution. Working alongside his new comrades, Kurou must defend his home and master his inherited power. The core team of Toutou Patriots includes Seiryumaru, the masked leader who belongs to a lineage where the name is passed down to protect the kingdom. Nishiki is the veteran who recruited Kurou, still haunted by witnessing Tsubame's death and frequently coughing up blood. Nagasu is a firefighter from Edo who wields a massive hammer. Usagi Kagura fights using a giant doll that becomes more powerful through magnetism by absorbing surrounding materials, while her brother Kikuro Kagura is an acclaimed actor who battles with an umbrella.

The central arc of FLAGS follows Kurou from his recruitment through his arrival at the Ouka tournament itself. As he struggles to unlock the Bansantou's eight forms, he confronts the truth of his father's death and faces opponents in the tournament arena. The initial chapters establish the team's unity, introducing their distinct fighting styles against the invading pirate threat. The manga then moves into the tournament proper, where Kurou and the Toutou Patriots face teams like the Tanalia team, with Kurou taking the stage for his first official battle. The story concludes with the tournament matches, as Kurou seeks to fulfill his promise to not only pass his trial but awaken all eight powers of the Bansantou to become the strongest Patriot of all.