Following a ruthless attack from an imperialist criminal gang known as the Masked Demons, Shinsengumi's Eighth Division—the law-enforcing squad in Kyoto that remains faithful to the shogunate—is nearly annihilated, with its sole survivor, Heisuke Toudou, critically injured. Urged to rebuild the Shinsengumi by the local feudal lord, Katamori Matsudaira, Toudou decides to offer eight convicts the chance to redeem themselves: they must abandon their old names and become substitutes for the eight Shinsengumi captains. All accept but one, who ends up immediately executed by the former assassin Sakuya. However, Toudou has a hard time transforming the seven reformed criminals into loyal servants. Due to his lack of discipline, the impulsive and vengeful Ichibanboshi, whose family perished at the hands of the Masked Demons, threatens the success of Toudou's strategy. As Toudou pledges to protect the shogunate against imperialists and foreign invaders, other factions, such as Kogorou Katsura's group, start to put their plans in motion with only one goal in mind—to seize power at the dusk of the Edo period.

Following the conclusion of the three-way organizational war, government bureaucrat Ango Sakaguchi recalls an event that transpired years ago, after the death of the former Port Mafia boss. Osamu Dazai, still a new recruit at the time, was tasked with investigating rumors related to a mysterious explosion that decimated part of the city years ago—and its connection to the alleged reappearance of the former boss. Due to circumstances out of his control, he is partnered with Chuuya Nakahara, the gifted yet impulsive leader of a rival clan known as the Sheep, to uncover the truth behind the case and shine a light on the myth of Arahabaki—the god of fire who might just lead Dazai to the case's solution. Meanwhile, in the present day, it is business as usual once again for the Armed Detective Agency. Their peaceful break will not last for long, however, as enemies old and new gather their strength and prepare for another face-off.

In the wake of an earthquake that devastated most of the city, Tokyo has been rebuilt in record time due to the development of humanoid robots known as boomers. After the disaster, these machines now service the city as cheap labor. Genom Corporation is the mastermind behind the boomers, having become so rich and powerful that they have extended its influence into space. However, all is not well with the boomers. Random breakdowns in their neural structure are causing some of them to go berserk, destroying property and killing humans in violent rampages. To combat this, Tokyo has formed the Advanced Police, a peacekeeping force with jurisdiction over boomer matters. There are also rumors of a second group known as the Knight Sabers, a vigilante unit operating from the shadows. Trying to investigate the Knight Sabers, the adventurous Linna Yamazaki travels to Tokyo in pursuit of her heroes. There, she finds the enigmatic singer Priscilla Asagiri, the beautiful entrepreneur Sylia Stingray, and the exuberant Nene Romanova, each with their own reasons for coming together. As the struggle intensifies, the girls learn that the boomer problem might delve deeper than any of them could ever imagine.

The two part finale of Buddy Complex television series deals with the final battle between the Free Treaty Alliance and the space division of Zogiria, lead by an elderly Bizon, as Earth and time itself hang in the balance.