In the distant future, humanity has been driven to near-extinction by giant beasts known as Klaxosaurs, forcing the surviving humans to take refuge in massive fortress cities called Plantations. Children raised here are trained to pilot giant mechas known as FranXX—the only weapons known to be effective against the Klaxosaurs—in boy-girl pairs. Bred for the sole purpose of piloting these machines, these children know nothing of the outside world and are only able to prove their existence by defending their race. Hiro, an aspiring FranXX pilot, has lost his motivation and self-confidence after failing an aptitude test. Skipping out on his class' graduation ceremony, Hiro retreats to a forest lake, where he encounters a mysterious girl with two horns growing out of her head. She introduces herself by her codename Zero Two, which is known to belong to an infamous FranXX pilot known as the Partner Killer. Before Hiro can digest the encounter, the Plantation is rocked by a sudden Klaxosaur attack. Zero Two engages the creature in her FranXX, but it is heavily damaged in the skirmish and crashes near Hiro. Finding her partner dead, Zero Two invites Hiro to pilot the mecha with her, and the duo easily defeats the Klaxosaur in the ensuing fight. With a new partner by his side, Hiro has been given a chance at redemption for his past failures, but at what cost?

Two years have passed since the CCG's raid on Anteiku. Although the atmosphere in Tokyo has changed drastically due to the increased influence of the CCG, ghouls continue to pose a problem as they have begun taking caution, especially the terrorist organization Aogiri Tree, who acknowledge the CCG's growing threat to their existence. The creation of a special team, known as the Quinx Squad, may provide the CCG with the push they need to exterminate Tokyo's unwanted residents. As humans who have undergone surgery in order to make use of the special abilities of ghouls, they participate in operations to eradicate the dangerous creatures. The leader of this group, Haise Sasaki, is a half-ghoul, half-human who has been trained by famed special class investigator, Kishou Arima. However, there's more to this young man than meets the eye, as unknown memories claw at his mind, slowly reminding him of the person he used to be.

Located on the outskirts of Tokyo, Hachimitsu Private Academy is a prestigious all-girls boarding school, famous for its high-quality education and disciplined students. However, this is all about to change due to the revision of the school's most iconic policy, as boys are now able to enroll as well. At the start of the first semester under this new decree, a mere five boys have been accepted, effectively splitting the student body into a ratio of two hundred girls to one boy. Kiyoshi, Gakuto, Shingo, Andre, and Jo are quickly cast away without having a chance to make any kind of a first impression. Unable to communicate with their fellow female students, the eager boys set their sights on a far more dangerous task: peeping into the girls' bath! It is only after their plan is thoroughly decimated by the infamous Underground Student Council that the motley crew find their freedom abruptly taken from them, as they are thrown into the school's prison with the sentence of an entire month as punishment. Thus begins the tale of the boys' harsh lives in Prison School, a righteous struggle that will ultimately test the bonds of friendship and perverted brotherhood.

With the introduction of strict new morality laws, Japan has become a nation cleansed of all that is obscene and impure. By monitoring citizens using special devices worn around their necks, authorities have taken extreme measures to ensure that society remains chaste. In this world of sexual suppression, Tanukichi Okuma—son of an infamous terrorist who opposed the chastity laws—has just entered high school, offering his help to the student council in order to get close to president Anna Nishikinomiya, his childhood friend and crush. Little does he know that the vice president Ayame Kajou has a secret identity: Blue Snow, a masked criminal dedicated to spreading lewd material amongst the sheltered public—and Tanukichi has caught the girl's interest due to his father's notoriety. Soon, Tanukichi is dragged into joining her organization called SOX, where he is forced to spread obscene propaganda, helping to launch an assault against the government's oppressive rule. With their school set as the first point of attack, Tanukichi will have to do the unthinkable when he realizes that their primary target is the person he admires most.