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.

Broadcasting club member Shihono Kobayashi always gushes to her friend Aoto Endou about MagiKoi, an otome game where protagonist Fiene attends the Royal Academy of Magic. But despite the colorful cast, the one character Kobayashi is most obsessed with is the villainess Lieselotte Riefenstahl. Contrary to her rude remarks toward Fiene, Lieselotte longs to be her friend. Lieselotte is also deeply in love with her own fiancé, Prince Siegwald Fitzenhagen—the game's main love interest. Unfortunately, in almost every route, Lieselotte is doomed to a tragic end. Kobayashi manages to convince Endou to play MagiKoi to practice his speaking skills. What begins as a normal playthrough turns extraordinary when Siegwald suddenly hears the players' voices inside the game! Now labeled as "gods," Endou and Kobayashi use their comments and analyses to save their beloved tsundere villainess from her fated demise.

Princess Anisphia "Anis" Wynn Palletia has always dreamed of flying through the sky, even though the people of her kingdom consider it a silly ambition. Also at odds with her goal is the fact that Anis is incapable of using magic despite her noble status. Refusing to give up so easily, she renounces her right to the throne, and focuses on developing "magicology" by combining various resources with knowledge from her previous life on Earth. Due to Anis' nature, responsibility for the kingdom's future is passed onto her younger brother, Algard. Pushed into a political marriage with Euphyllia Magenta, a girl he hardly knows, Algard rebels by spending more time with a commoner girl than his fiancée. After Euphyllia tries to intervene, Algard publicly calls off their marriage and denounces his ex-fiancée as a bully. After crashing into the banquet where Algard makes the announcement, Anis rescues Euphyllia on the flying broom she is testing. She decides to make Euphyllia her assistant, which the other girl reluctantly agrees to. Although their partnership appears random at first, Anis has an ulterior motive for wanting Euphyllia's company.

The hero king Inglis—who dedicated his entire life to building his country—is now approaching death. To award him for his honorable achievements, the goddess Alistia appears and grants him one wish. Having never been able to master the blade, Inglis asks to be reincarnated in order to do so. In a blink of an eye, Inglis finds himself born in the far future as a daughter of the Eucus noble family. Six years later, Inglis is discovered to be Runeless—incapable of utilizing the runes that enable the use of magic in this era. She is therefore ineligible to become a knight. However, this fits in well with Inglis' plan: she instead decides to become the squire for her cousin, Rafinha Bilford, allowing Inglis to focus on pushing her limits. For Inglis, the challenges this familiar yet different world has to offer are instead opportunities for her to hone her skills—and possibly become an extraordinary squire in the process.