Living in the slums of a wealthy town, Rudo and his foster father Regto try to coexist with the rest of the town's residents, but Rudo despises the wastefulness of the upper class. Ignoring the warnings from those around him, Rudo regularly rummages through the town's garbage in search of anything useful or valuable to save from the "Abyss"—a massive hole where anything considered trash is dumped, including people. Rudo's biological father was one such person, having been thrown into the Abyss after he was accused of murder. One day, after running into a mysterious figure on the way home, Rudo returns to find Regto's dying body on the floor. He is immediately found at the scene by the authorities and is charged with murder. No one believes his claims of innocence, and he is thrown into the Abyss. Instead of dying, however, he finds himself in a strange, foul-smelling place surrounded by monsters made out of trash. When Rudo is attacked by said monsters, he is saved by a man named Enjin, who reveals himself to be a "Cleaner"—someone who uses special weapons called Vital Instruments to combat these creatures. In order to get his revenge on the one who killed Regto, Rudo reluctantly becomes a Cleaner to fight his way back up and out of the Abyss.

After a strategic maneuver, Senkuu Ishigami's team stalls Dr. Xeno's more scientifically advanced forces. A ceasefire between the two factions allows for the establishment of Corn City in North America, a hope for a future thriving population. Meanwhile, Senkuu and some of his teammates rush toward the Amazon in South America—the epicenter of the petrification beam's impact—to create Superalloy City and progress their spaceship project. With dangerous enemies still pursuing Senkuu and his companions, it is a race against time to reach the heart of the dense Amazon. As unexpected allies and scientific creations further fuel this leg of their journey, Senkuu is closer than ever to finally uncovering the mystery behind the petrification phenomenon.

It has been six months since Yoshiki Tsujinaka's best friend, Hikaru Indou, went missing in the mountains and returned a week later with no recollection of what had transpired. Certain that it is not the Hikaru he knows who came back, Yoshiki finally asks Hikaru about it. Suddenly, "Hikaru" reveals his true monstrous form and begs Yoshiki to keep it a secret, as he does not want to kill him. Despite his paranormal nature, "Hikaru" seems almost innocent, full of childlike wonder and eager to experience the summer heat, the countryside, and all kinds of other things in a human body for the first time. And for Yoshiki, it matters little if "Hikaru" is a fake relying on stolen memories—as long as he never leaves again. As Yoshiki desperately clings to "Hikaru" in his intense grief, it becomes increasingly clear that something dangerous and supernatural may have descended from the mountains into their village.

After the success of his crowdfunded movie featuring the woman of his dreams, Chizuru Ichinose, university student Kazuya Kinoshita resumes his life of lies and deception. Although he pretends that he has been in an ideal relationship with Chizuru for more than a year, Kazuya still mostly sees her through a rental girlfriend company's services. However, after Kazuya attends a private party with Chizuru, he reaches the decision to finally confess his feelings to her. Unfortunately for him, his trial girlfriend Ruka Sarashina and his ex-girlfriend Mami Nanami continue to complicate his already messy attempts at romance. While he is forced to keep up his facade, Kazuya is under pressure to find a solution to his ever chaotic love life.