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.

Equipped with his passion for diving and admiration for marine biology, university student Tsuneo Suzukawa tries his best to juggle several part-time jobs to earn enough money to study abroad. But one night, in a fateful accident, he meets a girl in a wheelchair, driving his current path into a detour. The girl, Kumiko—who prefers to be called Josee—initially comes off as rude. Tsuneo, however, is then convinced by Josee's grandmother to take on the paid job to be Josee's caretaker. Despite being annoyed with her bossy demeanor, Tsuneo sees the opportunity to save more funds to support his academic dream. Nonetheless, after putting up with Josee's behavior for some time, Tsuneo tries to quit, only to discover Josee's dreams of traversing the outside world—to experience a life free from her crippling condition. Changing his mind, Tsuneo decides to accompany Josee in exploring the wonders that the world has to offer. Through their time together, the two begin to realize that the traits that bind them may be vital toward fulfilling their respective aspirations.

The entire countryside comes to a halt midday to witness a rare solar eclipse that is rumored to allow the average person to see Mushi. Unable to avert their gaze, the air is full of awe and wonder—but those who know the Mushi are preparing for the eclipse's aftermath. Based on a prediction from Tanyuu Karibusa, the cursed recorder, Mushishi Ginko finds himself in a very unlucky farming village. Immediately following the solar eclipse, a strange black cloud begins to gather in the sky and blocks the sun once more. Suspecting it to be the work of a Mushi known as Hihami, Ginko seeks to liberate the village from perpetual darkness. However, it seems that not all of the villagers are eager to return to the light.

Following the faceless god Hitogami's advice seems to have worked wonders for Rudeus Greyrat. After enrolling into the University of Magic as he was told, Rudeus reunites with his childhood friend Sylphiette, who put a valiant effort into curing his condition. The two grow ever closer together and decide to host a wedding party, inviting the friends they have made over the years to announce and formalize their relationship. For all his recent blessings, however, Rudeus' troubles are far from over. The research he is helping Shizuka Nanahoshi conduct hits a bottleneck, sending her into a deep slump much like he experienced in his previous life. Furthermore, a letter from his father, Paul, brings complications to Rudeus' relationships, and Sylphiette still knows next to nothing about his real background. In the face of these issues, Rudeus will have to apply the lessons he has learned in this new world to navigate through the challenges that come with living a life to its fullest.