Six months ago, Sakuta Azusagawa had a chance encounter with a bunny girl in a library. Ever since then, he's been blissfully happy with his girlfriend: Mai Sakurajima, that same bunny girl. However, the reappearance of his mysterious first crush, the now-adult Shouko Makinohara, adds a new complication to his relationship with Mai. To make matters worse, he then encounters a middle school Shouko in the hospital, suffering from a grave illness. Mysteriously, his old scars begin throbbing whenever he's near her. With Shouko's bizarre situation somehow revolving around him, Sakuta will need to come to terms with his own conflicting feelings, for better or worse. With a girl's life in his hands, just what can he do?

After the resolution of the debut, Kate and her Doll Emilico have officially become residents of the Shadows House. However, they are under constant vigilance by the Star Bearers—an elite group in charge of the children's wing. In order to escape from their surveillance and the morbid methods they use to keep everyone's loyalty in check, Kate and Emilico must be wary of who to trust and aim to become Star Bearers themselves. Meanwhile, the Star Bearers have encountered their own problems. A mysterious robed figure dubbed Master Robe has trespassed and roams around the children's wing. At first, Master Robe is deemed harmless, but more incidents start occurring that endanger the Dolls' lives—all of them pointing to the suspicious individual. To improve her reputation, Kate decides to solve the mystery herself. Yet, with so few clues and so many suspects, searching for Master Robe and their motive for attacking the mansion proves more challenging than she imagined.

The Shadows, characterized by their pitch-black appearance and tendency to emit soot when agitated, are a family of nobles who reside in a colossal manor deep within the mountains far from other humans. When a Shadow child is nearly of-age, they are assigned a Living Doll who acts not only as their attendant but also as their second half—the faces they could have had if not for their complexion. Emilico is a cheerful, newly created Doll who serves a rather soft-spoken master named Kate. Despite their difference in personalities, Emilico does what she can to carry out the needs of her master. As she learns more about her role and duty, Emilico begins to meet her fellow Dolls and their respective masters and comes to know more about the purpose of her existence. Do not fret over trivial matters, says one of the rules by which all Dolls must abide. But how could the ever-curious Emilico do so in the face of the deep secrets that the Shadows House holds?

Hana Ichinose, a 17-year-old high school student who is not only introverted, but also insecure and timid, has just moved and will be attending a new school. To make her situation more difficult, Hana is a slow start, which means that she missed a year and worries about attending a class where everyone is younger than her. During her introduction, the teacher reveals it is Hana's birthday, which gives her the jumping-off point to meet three of her classmates: Tamate Momochi, a charismatic and extroverted girl; Kanmuri Sengoku, who is shy and small; and the popular and pretty Eiko Tokura. Not wanting to lose the chance to make new friends, Hana's interactions with these three mark the beginning of some beautiful relationships that will change her life.