Many of us know what it is like to transition to a new school with few to no friends in a new environment, going through the arduous process of getting to know people again. Bocchi Hitori knows this struggle all too well, having just graduated from elementary school and thrown into middle school. Unfortunately, she suffers from extreme social anxiety: she faints when overwhelmed, vomits when nervous, and draws up ridiculously convoluted plans to avoid social contact. It does not help that her only friend from elementary school, Kai Yawara, will not be attending the same middle school as Bocchi. However, wanting to help her, Kai severs ties with Bocchi and promises to reconcile with her when she befriends all of her classmates in her new middle school class. Even though Bocchi has no faith in herself, she is determined to be friends with Kai again. Summoning all of her courage, Bocchi takes on the daunting challenge of making friends with her entire class, starting with the delinquent-looking girl sitting in front of her...

On the surface, the thought of Kyouko Hori and Izumi Miyamura getting along would be the last thing in people's minds. After all, Hori has a perfect combination of beauty and brains, while Miyamura appears meek and distant to his fellow classmates. However, a fateful meeting between the two lays both of their hidden selves bare. Even though she is popular at school, Hori has little time to socialize with her friends due to housework. On the other hand, Miyamura lives under the noses of his peers, his body bearing secret tattoos and piercings that make him look like a gentle delinquent. Having opposite personalities yet sharing odd similarities, the two quickly become friends and often spend time together in Hori's home. As they both emerge from their shells, they share with each other a side of themselves concealed from the outside world.

As the graduation ceremony at Katagiri High School comes to an end, Kyouko Hori, her boyfriend Izumi Miyamura, and their friends begin to look back on their time as students. The moments they shared together may be fleeting, but each one is a colorful piece of their precious memories.

The Abyss—a gaping chasm stretching down into the depths of the earth, filled with mysterious creatures and relics from a time long past. How did it come to be? What lies at the bottom? Countless brave individuals, known as Divers, have sought to solve these mysteries of the Abyss, fearlessly descending into its darkest realms. The best and bravest of the Divers, the White Whistles, are hailed as legends by those who remain on the surface. Riko, daughter of the missing White Whistle Lyza the Annihilator, aspires to become like her mother and explore the furthest reaches of the Abyss. However, just a novice Red Whistle herself, she is only permitted to roam its most upper layer. Even so, Riko has a chance encounter with a mysterious robot with the appearance of an ordinary young boy. She comes to name him Reg, and he has no recollection of the events preceding his discovery. Certain that the technology to create Reg must come from deep within the Abyss, the two decide to venture forth into the chasm to recover his memories and see the bottom of the great pit with their own eyes. However, they know not of the harsh reality that is the true existence of the Abyss.