Cyberpunk: Edgerunners tells a standalone story about a street kid trying to survive in a technology and body modification-obsessed city of the future. Having everything to lose, he chooses to stay alive by becoming an edgerunner—a mercenary outlaw also known as a cyberpunk.

Wataru Sajou is infamous in his school for persistently seeking the attention of his crush, Aika Natsukawa. His usual day revolves around shadowing her and confessing his undying love at every turn. However, a moment of epiphany leads Wataru to relinquish his childish behavior and face the reality that she will never return his one-sided feelings. He distances himself from Aika and spends his newfound spare time with his friends and in the company of other lovely girls. As Wataru moves on, Aika starts approaching him in unusually suggestive ways—making him question whether giving up on his love was the right decision after all.

Under the belief that the omnipotent god Mitama will come to save him, Yukito Urabe participates in a ritual to become the new leader of his father's cult. But when the boy drowns during the ritual, he wishes to be reborn in a world without gods or religion. Reawakening in a completely different world devoid of spirituality. He meets a deviant girl named Aruaru, who introduces him to her village. However, his idyllic image of this world's society is short-lived when he witnesses a public group suicide and learns of the country's end-of-life system: at any moment, the government may order any citizen to die. Aruaru and her sister are forcibly taken for execution soon after, prompting Yukito to rush to their rescue—but to no avail. In a moment of desperation, Yukito recalls his father's teachings and utters a prayer for Mitama to save them. Seemingly answering his call, a little girl descends from the sky and annihilates everyone who harmed Yukito and his friends. To Yukito's surprise, the girl introduces herself as Mitama.

High schooler Hayase Nagatoro loves to spend her free time doing one thing, and that is to bully her Senpai! After Nagatoro and her friends stumble upon the aspiring artist's drawings, they find enjoyment in mercilessly bullying the timid Senpai. Nagatoro resolves to continue her cruel game and visits him daily so that she can force Senpai into doing whatever interests her at the time, especially if it makes him uncomfortable. Slightly aroused by and somewhat fearful of Nagatoro, Senpai is constantly roped into her antics as his interests, hobbies, appearance, and even personality are used against him as she entertains herself at his expense. As time goes on, Senpai realizes that he doesn't dislike Nagatoro's presence, and the two of them develop an uneasy friendship as one patiently puts up with the antics of the other.