"Pankis! 2-jigen" centers on a group of high school students who discover a mysterious app that allows them to enter a two-dimensional world. This digital realm, known as "2-jigen," is a vibrant, pixelated universe where the laws of physics and reality are distorted. The protagonist, Haruto, stumbles upon the app after receiving a cryptic message on his phone. Alongside his friends, Yui, a tech-savvy classmate, and Riku, a competitive gamer, Haruto begins exploring the 2-jigen world, uncovering its secrets and the dangers it holds.

The narrative unfolds as the trio encounters various challenges within the 2-jigen world, including puzzles, battles with digital entities, and rival groups of users who seek to exploit the app's power. The app's origins remain shrouded in mystery, with hints suggesting it was created by a reclusive programmer who vanished years ago. As the group delves deeper, they uncover a connection between the app and a series of real-world disappearances, including that of Haruto's older brother, who went missing under similar circumstances.

Character dynamics play a significant role in the story. Haruto is driven by a desire to uncover the truth about his brother, while Yui provides technical expertise and a cautious approach to their adventures. Riku, on the other hand, is motivated by the thrill of competition and often clashes with Haruto over their differing priorities. The group's interactions with other app users, including a mysterious girl named Aoi who seems to know more about the 2-jigen world than she lets on, add layers of intrigue and tension.

The plot escalates as the group discovers that the 2-jigen world is not just a game but a testing ground for a larger experiment involving artificial intelligence and human consciousness. The stakes rise when they learn that prolonged exposure to the 2-jigen world can have irreversible effects on their minds and bodies. The series explores themes of identity, the boundaries between reality and virtuality, and the ethical implications of technological advancement.

As the story progresses, Haruto and his friends must confront the creator of the app, who reveals the true purpose behind the 2-jigen world. The final arc revolves around their efforts to dismantle the system and prevent its misuse, culminating in a high-stakes confrontation that tests their resolve and friendship. The series concludes with a resolution that ties together the central mysteries while leaving room for contemplation about the future of technology and its impact on humanity.