Ichiro Ohgami, having just been informed that he will be taking command of the secret corps known as the Imperial Flower Combat Troop, Flower Division, arrives in the imperial capital ("Teito", which is, well, Tokyo except not called that) and is taken to the Imperial Theatre by Sakura Shinguji, who is herself new to the team. Ohgami is greatly surprised to find that he has been posted to a theater, and doubly so when he's informed that he'll be filling the vital role of... clipping tickets of patrons as they come in. Fortunately for his patience, it doesn't take long for the city to come under attack by evil forces, and he's quickly informed of his real role and given a quick course on operating the Koubu. Combat ensues, but he's able to push them back, with the aid of Sakura, Maria Tachibana, Iris Chateaubriand, and Sumire Kanzaki.

Shortly after, Kohran Ri arrives from the Hanayashiki branch of the Imperial Flower Combat Troop, where she's been working on the development of the Koubu. Ohgami is also introduced to Ayame Fujieda, a woman of surpassing beauty and an air of serenity, and who incidentally happens to be the Vice Commander of the Flower Division. Ohgami winds up mooning over Fujieda a bit, making Sakura instantly jealous. A battle at Teito Tower is won, thanks to timely fire support from the Flower Division's flying battleship, the Shougei-Maru.

The next episode focuses on Maria, who is having trouble with Ohgami's leadership, which she sees as irresolute and reckless. Kanna Kirishima returns from her martial arts training, displaying incredible strength and an even more incredible appetite. In a battle against the Black Sanctum Council member Aoki Setsuna, a young child is threatened, and either Ohgami or Sakura is severely injured protecting him. Either way, Ohgami is treated to a severe tongue-lashing by Maria. Before the matter is resolved, Setsuna appears to Maria, threatening to reveal her past as "Kazuar", and Maria pursues him. (Naturally, this past is promptly revealed to Ohgami and the others.) The Flower Division tracks down Maria's Koubu, which she has abandoned, and follows a signal from her uniform's tracking device to where she has been captured by Setsuna. The following battle takes care of Setsuna.

Iris, by bullying Ohgami into agreeing to taking her out on a date in celebration of her birthday, manages to break up some private time between Sakura and Ohgami. The date proceeds well, until the two go to see a scary movie, at which point Iris panics. Her spiritual powers go out of control and a massive earthquake levels the theater. After being scolded, a despondent Iris barricades herself in her room, and none of the Flower Division's members are able to convince her to come out. She eventually flees the Imperial Theatre by commandeering her new Koubu and returns to the park where the date took place... coincidentally, just in time for an attack by Rasetsu. Ohgami and Sakura recover Iris, once she's calmed down somewhat, and the entire Division finishes off Rasetsu.

During the production of the play "Saiyuki", Kanna and Sumire get into a fight and nearly destroy the stage. Yoneda orders those two to accompany Ohgami in an investigation of an old abandoned mansion, which apparently holds the interest of the enemy. There, they discover Kanna's fear of snakes, Sumire's fear of spiders, and Crimson Miroku, who they promptly drive off with the assistance of the timely-delivered Koubu and the rest of the Flower Division.

The presentation of Saiyuki wraps up, much improved by Sumire's and Kanna's improved attitudes towards each other, and the Flower Division prepares for a party. However, Sakura's return from shopping for supplies is interrupted by a thunderstorm, and we learn that Sakura has a dire fear of thunder. Miroku, who tracked the Flower Division back to the Imperial Theatre, launches an all-out assault, trapping Ohgami and Sakura in one of the underground rooms while the others are left to fend off advancing hordes of enemy steam-powered weapons. Ohgami and Sakura escape through a one-in-a-million shot with Maria's practice gun, and Sakura's great amount of spiritual power is revealed in saving them from the ensuing explosion. Miroku's mecha is destroyed, but she escapes, and the enemy completes their plan of unsealing the evil energies of Teito. The shock of the evil energies knocks Sakura into a coma.

The leader of the Black Sanctum Council, Tenkai, proclaims that he wishes to re-establish the Tokugawa Shogunate, and that he will destroy Teito if it does not surrender. Kohran isolates an amazingly powerful source of evil and the Flower Division, believing it to be Tenkai's location, attacks. However, it's actually a trap set by Miroku, and they are besieged by countless numbers of the enemy. However, Sakura suddenly recovers and bails them out, and they retreat to plan a new attack. After the revelation of the backstory of the Kouma War five years ago, the enemy base is identified as caverns below the Japan Bridge. Tenkai is destroyed by the combined spiritual power of the Flower Division.

For the New Year, Ohgami gets to enjoy a day with the girl who likes him best, but they're interrupted by Aoi Satan, last survivor of the Black Sanctum Council, and his minions, the Kouma which had been banished five years ago. The Kouma are amazingly powerful, and a short battle with a few of them is enough to nearly wreck the Flower Division's Koubu units. As an attempt to increase their strength, the Flower Division separates to engage in special training. Sumire uses her influence in society to produce the funding needed for Kohran to produce a new version of the Koubu, named the Shinbu. The Shinbu prove much more capable of attacking the Kouma, and Aoi Satan's subordinate Inoshishi is destroyed.

In the background of a comedic play starring Kohran and Iris, Ohgami learns the rest of the history of the Kouma War. Yoneda also reveals to him the final trump card of humanity, the Majinki, which is three magical items capable of releasing immense spiritual power. Ayame falls under the influence of Aoi Satan and nearly strangles Ohgami, but recovers at the last second, and orders Ohgami to shoot her if it happens again. The Imperial Theatre is again attacked by one of Aoi Satan's subordinates, Shika, who is promptly killed. However, Ayame once again turns traitor, steals the Majinki, and reveals herself as a demon in alliance with Aoi Satan.

After doing some much-needed cheering up of the rest of the Division, Ohgami learns that Aoi Satan is about to use the Majinki to summon the Seima Castle from Tokyo Bay - a gigantic floating city equipped with a massive cannon that is fueled by negative human energies. However, they are forced to first deal with the final one of Aoi Satan's three henchmen, Chou, but they do not beat him in time to prevent the Seima Castle's revival.

Knowing that they don't have a chance, the Flower Division boards the Shougei-Maru and heads for the Seimajou. However, Yoneda has one last trick to play, and he orders the launch of the Aerial Battleship Mikasa... a steam-driven flying dreadnought over five miles long! The main cannon of the Mikasa blows away the gates of the Seima Castle, and the Flower Division infiltrates.

There, they find the three underlings of Aoi Satan once again revived, and the Flower Division girls sacrifice themselves one by one so that the rest of the group can advance. In the end, nobody is left but Ohgami and whichever girl is most attracted to him. They are confronted by Ayame, who refuses to return to normal despite Ohgami's entreaties, and Ohgami duels her and wins. He refuses to finish her off, though, and Ayame in turn saves him from Aoi Satan's attack. Aoi Satan is destroyed, but first he activates the fearsome main cannon of the Seima Castle. Yoneda is forced to ram the Mikasa into the Seimajou to prevent the destruction of Teito.

Aoi Satan reveals his true identity - as Satan! - and challenges Ohgami to a final showdown. Ayame rises, and tells Ohgami that her real name is Michael... the Archangel Michael... and that he has to stop Satan. She revives the members of the Flower Division, and Satan is destroyed. At the end, Michael offers Satan the forgiveness of Heaven, but he refuses, promising to return one day to afflict humanity once more.