On Christmas Eve, four-year-old Miri Unasaka arrives in Tokyo completely alone, in search of her father. The bright lights and merry atmosphere guide Miri to a big hotel and a man with a delicious-looking cake. However, the child has just unknowingly walked into the center of an elaborate, foolproof plan for assassinating a dangerous mafia boss. Professional assassins Kazuki Kurusu and Rei Suwa live together, fleeing memories of their grim childhoods and avoiding emotional connections. When their mission goes awry and they end up bringing Miri home, there is only one reasonable thing to do: return Miri to her mother. But the girl's innocent laugh and pure worldview quickly enamor her to Kazuki, who secretly enjoys playing a parent, and it is not long before Rei's impenetrable heart makes room for Miri. Miri's every move is unpredictable, and Kazuki and Rei find raising an energetic child harder than any of their missions. Although it presents a great risk to their careers, Kazuki and Rei—both assuming the affectionate nickname "papa"—decide to provide Miri with a normal childhood despite all the odds stacked against them.

Bayron City, a pioneering metropolis built on a newly discovered energy source, promises every citizen a luxurious and comfortable lifestyle. In reality, young demon exterminator Shuu Ogata's life is far from extravagant. Despite running a private military business, he often struggles to make ends meet due to reckless expenses. Fortunately, Kisara, his demon partner, is more than eager to help Shuu with household matters—albeit a little too forcefully for his comfort. The two work side by side, taking countermeasures against demon hazards, which stand as the biggest threats to the city. With danger lurking in the shadows, Shuu and Kisara strive to grant the town's safety; however, exterminating the possessed comes with a price unbeknownst to others.

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?

Jougorou Kobato has a habit of inserting himself into other people's problems. After realizing his detective skills are neither wanted nor appreciated, he makes an agreement with his shy friend Yuki Osanai to become ordinary together. Now entering high school, they aim to be perceived as regular people, yet Kobato cannot help but fall back into his deductive ways when faced with everyday mysteries. Unfortunately, mundane occurrences are not all the duo stumbles across. As they go through their school days trying to avoid drawing attention to themselves, Kobato and Osanai at times get caught up in incidents that put their plan of a peaceful, average life at risk.