Based upon the alluring story told in the first installment of the mega-popular Sakura Taisen video game series, the Sakura Wars TV series begins with the arrival of Sakura Shinguji in the Imperial Capital from her home in Sendai. Sakura is to take her place as a member of the Flower Division- a secret military unit that defends the Imperial Capital from the forces of evil with incredible steam-powered mecha called Koubu, as well as with their enormous spiritual powers. As a cover for the Flower Division’s covert operations, they also double as a theater troupe- performing some of the finest theatrical productions in all of Japan at the Great Imperial Theater, which doubles as their secret base of operations.

Sakura’s arrival at the Imperial Theater does not go off well, after she accidentally stumbles on stage in the midst of one of the Flower Division’s performances. Infuriated with the clumsy new arrival, her new teammates give Sakura the cold shoulder, making the girl feel unwanted. Disaster after disaster plagues Sakura wherever she goes, and after ruining Sumire’s press conference, and causing the Koubu to go berserk in the hanger below by her incredible spiritual power- Sakura takes flight from the Imperial Theater in tears.

Still wandering aimlessly through the city the next day, Sakura follows a man who likes strikingly similar to her deceased father to a small shrine amidst the city. There, she encounters the young boy who helped her earlier, and he brings the grief stricken Sakura home to him. Having convinced his mother to let her stay with them for a little while, Sakura breaks down in tears and is comforted by the boy’s mother. Elsewhere, the Flower Division meets to discuss Sakura’s disappearance. While the consensus seems that they could care less, Maria and Ayame meet privately to discuss the Sakura situation.

Back in the neighborhood where Sakura is staying, a Wakiji appears and begins reaping devastation throughout the area. Failing to convince the Flower Division to step in at their mobile command vehicle, Sakura takes up her sword and confronts the mechanical monster by herself. Having proven herself in the battle, Maria decides to extend to Sakura another chance. Sakura thanks the boy and his mother for their kindness, and moves back in to the Imperial Theater.

With a strict training regiment, both in operating the virtual Koubu and crafting herself in to a capable actress with the rest of the Flower Division, Sakura stumbles badly at both. Sakura is captivated by caliber of acting the others are capable of, and feels severely outmatched in skill. After witnessing Iris’s tenacity after injuring her ankle and still practicing relentlessly despite her serious injury, Sakura realizes just how much inner strength she’s going to need if she’s to make it as a member of the Flower Division. The next day, to everyone’s acknowledgement, Sakura is beginning to show signs of improving.

Later that night, another mechanical beast is rampaging through the city. Defying orders to stay and look after Iris, Sakura charges on to the battlefield to help her struggling comrades. While her charge started out heroic, the end result was nothing short of an abysmal failure. Feeling that a change in leadership is needed, General Yoneda and Major Fujieda ask Count Hanakogi, the Flower Division’s benefactor, to seek out someone better suited to command the Flower Division, both on and off the battlefield. The search narrows down to just two young Imperial Navy officers- Yuichi Kayama and Ichiro Ohgami.