Fuuta-kun has never owned a cat before, but his younger sister, Pii-chan, moves into his house with the round gray cat Kyuruga. Inexperienced with cats, Fuuta-kun has no idea what to expect, and each night after he returns home is marked by odd and endearing surprises from his new pet.

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.

Sentenced to death, ninja Gabimaru the Hollow finds himself apathetic. After leading a blood-soaked life, Gabimaru believes he deserves to die. However, every attempt to execute him inexplicably fails. Finally, Sagiri Yamada Asaemon, a fledgling member of a famed executioner clan, is asked to take Gabimaru's life; yet Sagiri makes no move to kill him as requested. Insisting that Gabimaru will not die because of his love for his wife, Sagiri instead offers him the chance to obtain a full pardon for his crimes. If he can travel to the island of Shinsekyo and obtain the Elixir of Life—which supposedly grants immortality—and bring it back for the shogun, then his freedom will be assured. But of the many who have traveled to Shinsekyo in search of the mythical Elixir, not a single person has returned sound of mind, if at all. Though unaware of the numerous dangers ahead, Gabimaru decides to accept the offer—alongside ten other death row convicts—in hope that he and his wife may finally live in peace.

Now in possession of the Edens Zero, Shiki Granbell has gathered the Four Shining Stars. With the help of his new friends, Shiki will be able to breach Dragonfall—the border of the Sakura Cosmos swarming with mechanical dragons. Once that is achieved, he can continue his quest to find the goddess Mother. Before the Edens Zero crew can advance their journey, they notice a mysterious warship following them. Upon learning that the ship—the Belial Gore—belongs to Drakken Joe, Shiki and his crew attempt to infiltrate it, intent on figuring out why the Dark Alchemist is after them. In the process, the Edens Zero is taken hostage by Drakken's subordinates. Though they are in a tight situation, Shiki refuses to back down. Working together with his friends, Shiki will have to take down the Dark Alchemist if he hopes to make it out of the Belial Gore alive.