Twenty-two-year-old college dropout Tatsuhiro Satou has been a hikikomori for almost four years now. In his isolation, he has come to believe in many obscure conspiracy theories, but there is one in particular which he holds unshakable faith in: the theory that the evil conspirator behind his shut-in NEET (Not in Employment, Education or Training) status is the Nihon Hikikomori Kyokai (NHK)—an evil and secret organization dedicated to fostering the spread of hikikomori culture. NHK ni Youkoso! is a psychological dramedy that follows Tatsuhiro as he strives to escape from the NHK's wicked machinations and the disease of self-wrought isolation, while struggling to even just leave his apartment and find a job. His unexpected encounter with the mysterious Misaki Nakahara might signal a reversal of fortune for Tatsuhiro, but with this meeting comes the inevitable cost of having to face his greatest fear—society.

Although her name means snow white, Shirayuki is a cheerful, red-haired girl living in the country of Tanbarun who works diligently as an apothecary at her herbal shop. Her life changes drastically when she is noticed by the silly prince of Tanbarun, Prince Raji, who then tries to force her to become his concubine. Unwilling to give up her freedom, Shirayuki cuts her long red hair and escapes into the forest, where she is rescued from Raji by Zen Wistalia, the second prince of a neighboring country, and his two aides. Hoping to repay her debt to the trio someday, Shirayuki sets her sights on pursuing a career as the court herbalist in Zen's country, Clarines. Akagami no Shirayuki-hime depicts Shirayuki's journey toward a new life at the royal palace of Clarines, as well as Zen's endeavor to become a prince worthy of his title. As loyal friendships are forged and deadly enemies formed, Shirayuki and Zen slowly learn to support each other as they walk their own paths.

To the outside world, Hanabi Yasuraoka and Mugi Awaya are the perfect couple. But in reality, they just share the same secret pain: they are both in love with other people they cannot be with. Hanabi has loved her childhood friend and neighbor Narumi Kanai for as long as she can remember, so she is elated to discover that he is her new homeroom teacher. However, Narumi is soon noticed by the music teacher, Akane Minagawa, and a relationship begins to blossom between them, much to Hanabi's dismay. Mugi was tutored by Akane in middle school, and has been in love with her since then. Through a chance meeting in the hallway, he encounters Hanabi. As these two lonely souls spend more time together, they decide to use each other as a substitute for the one they truly love, sharing physical intimacy with one another in order to stave off their loneliness.

In the year 2029, Niihama City has become a technologically advanced metropolis. Due to great improvements in cybernetics, its citizens are able to replace their limbs with robotic parts. The world is now more interconnected than ever before, and the city's Public Security Section 9 is responsible for combating corruption, terrorism, and other dangerous threats following this shift toward globalization. The strong-willed Major Motoko Kusanagi of Section 9 spearheads a case involving a mysterious hacker known only as the Puppet Master, who leaves a trail of victims stripped of their memories. Like many in this futuristic world, the Puppet Master's body is almost entirely robotic, giving them incredible power. As Motoko and her subordinates follow the enigmatic criminal's trail, other parties—including Section 6—start to get involved, forcing her to confront the extremely complicated nature of the case. Pondering about various philosophical questions, such as her own life's meaning, Motoko soon realizes that the one who will provide these answers is none other than the Puppet Master themself.