After surviving the brutal challenges of Idofront, Riko now possesses a White Whistle, allowing her to descend into the Abyss's sixth layer—The Capital of the Unreturned. Alongside Reg and Nanachi, Riko begins to explore the uncharted domain, where the ruins of the promised Golden City are located. As the trio starts to adapt to the harsh environment, they soon encounter dangerous creatures and treacherous landscapes. Their expedition leads them to a village inhabited by strange beings known as hollows. Despite the creeping sense of unease that welcomes them, the three venture onward to uncover the mysteries of the settlement and long-lost legacies of the forgotten adventurers who once descended into the horrors of the unexplored Abyss.

The bustling metropolis of Kansai, where cybernetic screens litter the neon landscape, may seem like a technological utopia at first glance. But in the dark alleys around the brightly-lit buildings, an unforgiving criminal underbelly still exists in the form of fugitives known as Akudama. No stranger to these individuals, Kansai police begin the countdown to the public execution of an infamous Akudama Cutthroat, guilty of killing 999 people. However, a mysterious message is sent to several elite Akudama, enlisting them to free Cutthroat for a substantial amount of money. An invisible hand seeks to gather these dangerous personas in one place, ensuring that the execution is well underway to becoming a full-blown bloodbath.

On her way to school one day, Suzume Iwato stumbles upon Souta Munakata, a young man searching for abandoned areas. The high school girl directs Souta to a nearby ruin, but out of pure curiosity, she herself decides to head to the same destination. Once there, Suzume discovers an isolated door with a dreamlike universe lying beyond it—a place that she can see and feel, but not enter. A strange stone rests on the ground nearby, but it turns into a cat-like creature and scurries away when Suzume lifts it. Suddenly afraid, she heads back toward her school, not realizing that her act of leaving the door open will have consequences. With the keystone released, the evil within the other universe can now freely escape and wreak havoc throughout Japan. Intending to correct her dangerous mistake, Suzume joins Souta—whose true goal is to prevent evil from festering—in finding and locking all open doors before the country is destroyed.

On the hot summer day of August 14, Shintarou Kisaragi is forced to leave his room for the first time in two years. While arguing with the cyber girl Ene who lives in his computer, Shintarou Kisaragi accidentally spills soda all over his keyboard. Though they try to find a replacement online, most stores are closed due to the Obon festival, leaving them with no other choice but to visit the local department store. Venturing outside makes Shintarou extremely anxious, but the thought of living without his computer is even worse. It's just his luck that on the day he finally goes out, he's caught in a terrifying hostage situation. Luckily, a group of teenagers with mysterious eye powers, who call themselves the Mekakushi Dan, assist Shintarou in resolving the situation. As a result, he is forced to join their group, along with Ene. Their abilities seem to be like pieces of a puzzle, connecting one another, and as each member's past is unveiled, the secret that ties them together is slowly brought to light.