At Suimei High, the Sakura-sou dormitory is infamous for housing the school's most notorious delinquents. Thus, when the relatively tame Sorata Kanda is transferred to the dorm, escaping this insane asylum becomes his foremost goal. Trapped there for the time being, he must learn how to deal with his fellow residents, including bubbly animator Misaki Kamiigusa, charming playboy writer Jin Mitaka, and the ever-reclusive Ryuunosuke Akasaka. Surrounded by weirdness, Sorata frequently finds respite in his interactions with his one "normal" friend, aspiring voice actress Nanami Aoyama. When Mashiro Shiina—a new foreign exchange student—joins the dormitory, Sorata is instantly enraptured by her beauty. Underneath her otherworldly appearance, Mashiro is an autistic savant, capable of world-renowned brilliance in her art, yet unable to perform simple daily tasks. After Sorata ends up in charge of taking care of Mashiro, the two inevitably grow closer, with Sorata's initial desire to escape the dormitory becoming a forgotten goal. Despite their eccentricities, every resident is incredible in their own field, leaving Sorata to contend with his own lack of any particular skill. With brilliance all around him, he thus strives to become an equal to their talent. Revolving around the hardships and joys of its colorful cast, Sakura-sou no Pet na Kanojo is a heartwarming coming-of-age tale of friendship, love, ambition, and heartbreak—through the lens of an ordinary person surrounded by the extraordinary.

Denizens from the Crimson Realm continue to infiltrate Misaki City and steal life energy from humans. To combat this threat, Flame Hazes are tasked with saving humans from losing their existences. But while it is a Flame Haze's duty to protect humans, Shana—the "Flame-Haired Burning-Eyed Hunter"—seems to be focusing her attention on one human in particular: Yuuji Sakai, a teenage boy who was unwittingly dragged into the fight between Crimson Denizens and Flame Hazes. Since her first encounter with Yuuji, Shana has started to see him as more than just a friend. In fact, Yuuji wonders if Shana might have revealed her feelings to him once before, but it is difficult for him to confirm due to her hot-and-cold personality. Nonetheless, their days pass like any other, until a new transfer student arrives at their high school—one who bears a striking resemblance to an old enemy. Yuuji and Shana have no time to dance around their feelings for each other; while their adversaries from the Bal Masqué organization plan their next attack, the two must keep their guard up as they explore the origin behind the coveted magical object within Yuuji's body, the "Midnight Lost Child."

Hushed exchanges among the female student populace of Shinyo Academy center around an enigmatic supernatural entity. This entity is Boogiepop, a Shinigami who is rumored to murder people at the height of their beauty before their allure wanes. Few know of his true nature: a guardian who, between periods of dormancy, manifests as the alter ego of a high school girl named Touka Miyashita to fend off "the enemies of the world." Now, a string of mysterious disappearances—presumed by the school to be merely runaways—has caused Boogiepop to awaken. But somewhere in the academy, a menacing creature hides, waiting for its opportune moment to strike. Boogiepop wa Warawanai subtly explores the intrinsic associations between human beings and their perception of time, while delving into its characters' complex relationships, emotions, memories, and pasts.

Although peace has finally returned to Ikebukuro, many of the odd occurrences have become common sights around the city. One such case is the police's constant pursuit of Celty Sturluson, the Headless Rider. Moreover, someone has placed a large bounty on her, igniting the motivation of gang members all over to begin searching for the supernatural creature as well. Meanwhile, Mikado Ryuugamine is approached by Aoba Kuronuma, a mysterious underclassman with unknown intentions, who reveals that he knows Mikado's true identity. But Ikebukuro's state of tranquility is short-lived, as a new threat appears in the form of a murderer who goes by the pseudonym "Hollywood," known for wearing a different mask each time they commit a crime. As the various events taking place prove to be connected yet again, Ikebukuro is thrown into another conflict that threatens to engulf the entire city in chaos.