After their long and tumultuous relationship, Koyomi Araragi and Hitagi Senjougahara are finally married. Their honeymoon, however, is far from ordinary. Accompanied by the vampire Shinobu Oshino, whom Koyomi plans to formally adopt as his daughter, and their kouhai Suruga Kanbaru, the newlyweds set off on a trip that doubles as an investigation into a rumored supernatural oddity connected to a killing stone. Koyomi, now an FBI apprentice living apart from Hitagi due to their careers, hopes this journey will be the perfect moment to discuss the sensitive topic of adopting Shinobu with his wife.

The story, titled Hitagi Honeymoon, primarily takes place during this two-day, three-night trip. Before departing, Koyomi reconnects with old acquaintances, including the now physically mature but mentally childlike Mayoi Hachikuji and the reclusive Sodachi Oikura. Once on the road, the dynamic is unusual yet familiar: Hitagi drives while Shinobu sits in a baby seat, and Kanbaru, now in her fifth year of medical school, joins the party. The central conflict emerges from Koyomi's internal struggle. He wishes to give Shinobu his family name, but Shinobu, burdened by her past sins of consuming humans, rejects the idea, believing she does not deserve such a place in his life. After a moment of tension, she retreats into Koyomi's shadow and refuses to emerge.

Seeking guidance, Koyomi turns to an internalized version of Tsubasa Hanekawa, who helps him realize that his plan for Shinobu must first be accepted by Shinobu herself, not just Hitagi. As a storm rolls in, blocking their view of the stars at the scenic Senjougahara landmark, a surprising resolution unfolds. It is Hitagi who reveals she has long anticipated this desire and proposes the adoption as a practical solution. She declares that if she can forgive her own mother for past wrongs, she can certainly accept Shinobu into their family. Moved, Shinobu uses a legendary sword called Nenekirimaru to part the rain clouds, revealing the night sky.

The honeymoon concludes with a new family bond formed, but the aftermath introduces a major shift in the series' status quo. The dramatic display of supernatural power attracts the attention of authorities, and a coincidental economic crisis implicates Hitagi's company. As a result, Koyomi, Hitagi, and Shinobu are placed into a witness protection program, forcing them to abandon their names and identities. The novel ends with a direct address to the reader, stating that the characters must go silent for a while and that they will adopt new names, leaving their future appearances in the series ambiguous. This installment, the first in the Family Season, sets the stage for a new era where the protagonist's original name may no longer be used.