The first volume in Inio Asano's manga series follows Punpun Punyama, an elementary school boy living in a densely packed residential neighborhood in Japan. Punpun is depicted not as a realistically drawn character but as a simple, cartoonish bird figure, while everyone around him is rendered in detailed, realistic art. This visual contrast externalizes Punpun's sense of alienation as he confronts family dysfunction, first love, and the slow erosion of innocence.
Punpun's school life begins with a loss: Miyo Ohta, the class sweetheart, is transferring away. That same day, a new transfer student, Aiko Tanaka from Nerima Prefecture, joins the class. The teacher assigns an essay about the students' dreams, and Punpun experiences love at first sight. Walking home, Aiko tells him the Earth will soon run out of oil and humanity will need to move to another planet. Punpun's heart beats so fast he feels like he is going to fly away. In class, after Punpun confesses his feelings by nodding, Aiko takes his hand and encourages him to speak up about his dream to save humanity, declaring that "people who discourage others will never find their own happiness." Her hand feels soft, warm, and small, and Punpun does not want to let go.
At home, Punpun's world is fracturing. His father has attacked his mother, and the police are holding his father while officers question Punpun. Uncle Yuichi, Punpun's unemployed uncle, arrives to pick him up and soon moves into the household. Punpun's aunt informs him he will now be known as Punpun Onodera, reflecting the divorce proceedings. When the teacher calls on Punpun to read his essay, his real dream is to become a space expert, but a classmate mocks the idea as impossible. Noticing Aiko watching, Punpun lies, saying his dream is to work in an average office and have an average family. Aiko confronts him afterward, calling him a coward and a liar.
Uncle Yuichi becomes a steady presence. He teaches Punpun a chant: "Dear God, dear God, tinkle hoy," promising that if Punpun gets lonely, God will appear. When Punpun uses the chant, God manifests as a smiling man with an afro and glasses who speaks in a casual, sometimes evasive manner. Punpun's father remains absent, explained away as having been "transferred for work."
Punpun's circle of friends provides companionship and comic relief. Seki is a tough boy whose family once ran a bento shop; Shimizu is a habitual liar who claims to communicate with the "Poop God"; Komatsu is athletic and easygoing; and Harumi rounds out the group. Punpun experiences his first sexual arousal and panics, convinced his brain has melted. Uncle Yuichi reassures him and provides educational books. Uncle Yuichi also gives Punpun a telescope. Looking through it one night, Punpun becomes convinced he has discovered a new planet, which he names "Planet Punpun." He fantasizes about winning the Nobel Prize and building a house on the planet where he would live with Aiko.
Aiko engineers a moment alone with Punpun by pretending to fall and getting sent to the nurse's office. She asks if he likes her; he nods. She says she likes him too, but her affection takes a possessive turn: She declares that everyone else can die as long as she has Punpun and demands that he think only about making her happy "forever and ever."
The kids discover a mysterious VHS tape on the street. Playing it at Seki's place, they watch a man confess to murdering his family and hiding three bodies in an abandoned miso factory, claiming to have left cash there as well. Separately, Aiko confronts Punpun again, revealing she has transferred to multiple schools and never wanted classmates to see her troubled home life. She tells Punpun she wants to go to Kagoshima, a city far to the south, to visit her uncle, a wealthy doctor. She asks Punpun to come with her, and he eagerly promises to go after the semester ends. Aiko warns him against betraying her again, and Punpun privately interprets the warning as a death threat. He holds her hand as hard as he can, feeling she would disappear if he let go.
Punpun places all his hopes on the miso factory: If they find money, he can take Aiko to Kagoshima. Seki reveals he knows the factory's location because the owner and his father were once friends; when the factory went bankrupt, it dragged his family's bento shop down too. Before the expedition, Harumi announces he is transferring schools and gives Punpun his bicycle as a farewell gift.
The group travels by bus to the factory, where Aiko spots them and decides to tag along. Inside the decrepit building, they find what appears to be a bloodstain but no bodies or money. A frightening figure appears, and the kids scatter in panic. A fire breaks out, but rain limits its spread, and the children escape shaken but safe. A television news report later confirms the murders were real: A man turned himself in, and the bodies were found in the factory.
After the ordeal, Punpun and Aiko sit together under a sky packed with stars. Punpun holds her hand and thinks, "The sky is so full of stars it's about to overflow. I hope I get to see it again someday." God appears looking unusually serious and tells Punpun that humans carry an emptiness that can never be filled, that people need and hurt each other but can never achieve perfect understanding. Then God tells Punpun to lighten up and asks to stay friends. Flashbacks trace the arc of Punpun's parents' marriage: His father once pledged to build a happy home, but after a layoff the marriage collapsed, with Punpun's mother calling it a mistake and saying she never should have had a child.
Punpun's mother is hospitalized after falling from a third-floor balcony at home. She claims her hand slipped, but Punpun's aunt suspects the fall was deliberate. The aunt, who once wandered abroad in her late teens in a restless search for freedom and happiness, stays to look after Punpun. He realizes he cannot deliver on his promise to take Aiko to Kagoshima, and the thought almost makes him cry. Yet part of him does not care, and he resents that he might be killed over a broken promise.
On the last day before summer vacation, Punpun finds a note from Aiko in his desk: "I'll be waiting at Town Hall at 6pm." Before he can act, his uncle rushes him to the hospital after his mother falls again, this time from a fire escape. He never goes to the meeting spot. Summer passes. On the first day of the new term, Aiko comes to school as usual, indicating she did not leave for Kagoshima alone. Punpun still loves her but is consumed by guilt.
Punpun's father visits him near the house but cannot come closer because of the separation. He confesses that his feeling of wanting to treasure Punpun's mother was real, even as he admits he is thoughtless and gets involved with whoever is convenient. He tells Punpun to fight on.
Two years pass. Punpun, now in middle school, has joined the badminton club at Komatsu's suggestion. Komatsu excels quickly while Punpun is stuck doing practice swings. Punpun still loves Aiko, but they have not spoken in two years. He feels completely alone. One day after school, he climbs to a high vantage point and looks out over the city. The silence of the empty school feels like "the world after humanity had been destroyed." The world stretches far beyond anything he imagined, and he declares he will become a grown-up starting today. God appears and mocks him: "See, you're such a child." Punpun tells God to shut up. Despite his defiance, it feels like his heart is being squeezed. The volume closes with Punpun suspended between his determination to grow up and the loneliness that continues to define his world.