Yūta Akikawa is a school-aged boy struggling with a deep fear of computers, rooted in childhood trauma. This technophobia poses daily challenges after his family moves to Kamimai City, a cutting-edge technological hub where computers are essential for everyday life and education, especially within his school.

His life shifts dramatically when a mysterious encrypted message appears on his cell phone. Opening it transports him into the Net World, a digital dimension existing within the internet and connected technologies. There, he meets three sentient programs called Net Ghosts—Pit, Pot, and Pat—collectively nicknamed "PiPoPa" (a name they resent). They reveal the nature of this digital realm to him.

Initially, Yūta keeps his discovery of the Net World a secret. He starts using his access to help others, fixing technological malfunctions and disruptions, often inadvertently caused or worsened by the PiPoPa trio. Repeated journeys into the Net World alongside PiPoPa allow Yūta to gradually confront and overcome his deep-seated technophobia, experiencing technology in a new, tangible way that fosters personal growth.

His character arc evolves significantly from avoidance to proactive engagement. He masters managing the PiPoPa ghosts' chaotic tendencies, directing their abilities toward solving problems. This responsibility accelerates his maturity, transforming him from a passive observer into an active participant and leader within the Net World. His mission expands from personal adaptation to defending the Net World against external threats, including schemes by the corporation Dream Future and the emergence of "Divine Forest"—his friend Mamoru Shindō possessed by his grandfather, Dr. Forest.

Key relationships shape his experiences. Hikaru Sofue, the first person he meets in Kamimai City, becomes his classmate and guide to the city's technology, eventually gaining access to the Net World with her own Net Ghost, Ecolon. His childhood friend Mamoru Shindō, a computer programming expert who once taught him basic skills, makes Mamoru's transformation into Divine Forest deeply personal. Classmate and bully Kazushige Enoshima adds interpersonal tension, often involving Hikaru and transfer student Sayaka Erenkova, who operates as the Net Ghost Web Venus.

His family background informs his interests and struggles. His father, Kenta Akikawa, is a photographer; Yūta shares his passion for astronomy, finding solace in stargazing. His mother, Yūko Akikawa, works as a programmer at Dream Future Japan, creating a stark contrast with his technophobia.

A major turning point arrives with Pū (also known as Seiren), a powerful Net Ghost linked to Dream Future's secret "Project Siren," whose initial presence destabilizes the Net World. Recognizing the true threat lies with humans misusing her abilities, Yūta and PiPoPa protect Pū. Her eventual Heroic Sacrifice to save the Net World from corrupted copies of herself destroys the original Net Dive connection, severing the human and Net Worlds—a profound loss for Yūta and his companions. However, a message left by Pū ultimately forges a new link, restoring access between the worlds.

By the series end, Yūta has transformed from a boy paralyzed by fear into a capable individual navigating both the physical and digital realms. He balances real-world responsibilities with his ongoing mission to safeguard the Net World alongside PiPoPa and the human friends who have joined the endeavor.