On a sunny July day in the 41st year of the Shinka Era, Jirou Hitoyoshi is tasked with covertly listening in on a secret meeting between a top government scientist and an industrial spy. However, his cover is blown, and the spy reveals himself to be an alien in disguise. Amidst the ensuing chaos, Jirou enlists the aid of cafe waitress and magical girl Kikko Hoshino, one of many superhumans who blend into society and secretly protect humanity from extraterrestrial threats. As a member of the government agency known as the Super Population Research Laboratory, Jirou has the dual task of protecting superhumans that defend humanity and disposing of any deemed too dangerous to live. Having proven herself a worthy ally, Kikko is invited to join the agency as its newest recruit. Fast forward five years: disapproval and distaste for superhumans are now commonplace in Tokyo. From government corruption and conflicting ideas of justice, to the morality of superhuman rights, the relationship between humans and the supernatural minority balances precariously in a world pervaded by whispers of unrest and unease. Under mysterious circumstances, Jirou has betrayed the agency, and is now a fugitive on the run. As he skulks through the rainy back alleys of Shinjuku, he is pursued by the very same superhumans that he himself once recruited.

Tricked into assassinating his own prospective father-in-law, righteous samurai Raizou Kurima is overwhelmed with guilt. In order to reclaim his honor, Raizou swears vengeance on the lord who gave him those misleading orders. In his pursuit, he is aided by self-proclaimed merchant-of-all-trades Yuuen Usui, who is actually one of the Revengers—assassins who seek justice for the wronged and dispense bloody revenge on their behalf. Tragedy seems destined to follow Raizou as he becomes increasingly intertwined with members of the Revengers. As he begins working as a vigilante alongside them, the complicated web between the corrupt Japanese political elite, the unscrupulous Europeans, and the Revengers gradually reveals itself. The more entangled he becomes in these affairs, the more Raizou realizes that justice is as deceptive as the honor that he sought to redeem.

Within Cardia Beckford's hazy memories, she can recall her father Isaac and the home where she lives alone, feared as a monster by the townsfolk—for in her body, she carries a deadly substance. Embedded in her chest by her father, the eternally beating heart—also known as Horologium—has the capability to produce infinite power. However, it also makes her skin destroy anything it touches. Many in London seek the Horologium, including the terrorist organization Twilight, with whom Isaac is rumored to have close ties. To obtain the Horologium's power, the British military forces Cardia to leave her home as their prisoner. But on the road, she is whisked away by the gentleman thief Arsène Lupin, who says he will steal her heart. Joining Lupin and his companions, Cardia begins a journey to discover the truth behind Isaac's connection with Twilight, her missing memories, and the Horologium within her chest.

For generations, the Bernstein family has been recognized as a house of nobles who favor books over everything else. Elianna Bernstein, daughter of a baron of the Sauslind Kingdom, is no different. But instead of being called a bookworm, she is known as the Bibliophile Princess. Four years ago, the crown prince, Christopher Selkirk Asherald, offered Elianna a special arrangement: if she would become his fiancée, he promised that she could continue to spend all her free time reading. Despite having to inherit a title of great responsibility, she agreed to the proposal, enticed by the prospect of gaining access to the royal archives housing a wide selection of books. To this day, Elianna firmly believes that her engagement is void of romantic sentiment. When she notices Christopher's interactions with another girl, she presumes that the days she spends with him will soon reach an end. Yet, during this period of uncertainty, Elianna and Christopher open a new chapter in their relationship, gradually uncovering their genuine feelings as they grow to better understand each other.