In a near-future Japan where technology has advanced to include home bio-printers capable of creating living creatures, a terrain designer named Sato attempts to print a Shiba Inu companion. Due to an error in the complex printing process, the result is not a dog but a completely unknown life form: a soft, squishy, loaf-shaped being never seen before. Despite the failed print, Sato becomes endeared to the strange creature. His friend Shiono is also charmed and gives it the perfect name Mochimochi (or Suama in the original Japanese), derived from the Japanese word for the soft, chewy rice cake.

The main character, Sato (designated Sato 46), works as a terrain designer and lives a quiet, routine life with few personal attachments. He is somewhat asocial and has little interest in food or interior decoration. His only friend is the loud and optimistic Shiono (Shiono 1), a junk dealer with a high level of technical skill who often teases Sato. The creature Mochimochi is a member of a newly registered species called Printernia Nippon. It is affectionate toward Sato, obtains nutrition through photosynthesis but also requires a special sugar supplement. A constant presence in their lives is nn266e38, Sato's designated Life Improvement Consultant, a being that monitors his health and daily activities, often seen physically interacting with Mochimochi.

As the story progresses, Sato discovers that other people have also experienced printer errors, resulting in unique creatures like his own. The cast expands to include individuals like Takagi (Takagi 11), the former CEO of the bio-printer company who knowingly released the flawed product; Tono (Tono 70), a veterinarian assigned by the Council to work at a factory site; Seta (Seta 8), a young man who was promoted to Sato's high-level residential area after working in hazardous reclamation zones; and Mukai (Mukai 62), a quiet, one-eyed miner who owns a shaggy, long-haired Printernia Nippon named Monaka.

The setting of Printernia Nippon is a deceptively peaceful dystopia. Society is rigidly managed, with citizens identified by numbers and living under constant surveillance by robotic "Watch Cats." A mysterious entity known as the Council governs the world. Outside the safe residential zones lie "reclaimed lands," contaminated areas where people must wear protective suits to work on environmental restoration. These lands are also home to dangerous remnants of a past conflict. The phrase "BIG CAT WATCHING YOU" is displayed in Sato's apartment, a direct reference to the iconic slogan from George Orwell's 1984, highlighting the oppressive nature of their seemingly idyllic world.

One of the first notable narrative arcs begins when Sato learns there are other people who printed unique creatures like Mochimochi. His social circle begins to grow as he connects with these individuals, leading to more questions about the true nature of his peculiar printed companion. Another significant arc revolves around the "Retrospective Festival," during which Sato demonstrates unexpected skills by skillfully operating a food printer and modeling a spirit ship. This event leads to an incident where the tiny green Printernia Nippon named Soramame goes missing, forcing the group to work together. As the series continues, the narrative explores the history of their world, revealing evidence of a massive, civilization-ending catastrophe, strongly implied to be a nuclear war. The story also delves into the true nature of the Council, which is heavily implied to be an artificial intelligence that survived the apocalypse and, feeling lonely, recreated humanity and now guides its "evolution" toward becoming morally good people. The creatures themselves grow more complex, with Mochimochi showing a strong will to protect Sato and later manifesting a large, muscular humanoid avatar named Mukima in virtual spaces.