Nobita Nobi argues that dinosaurs still exist, Suneo Honegawa quickly counters, while Takeshi Goda and Shizuka side with him. He asks Doraemon for help, but he is later convinced by Doraemon's gadget that dinosaurs are extinct when he asks whether there are dinosaurs alive 'on' earth. Meanwhile, Nobita must find a way to hide his test papers from his mom, a small battle of everyday life that quietly frames the bigger adventure to come.
As the day unfolds, while playing with Suneo's remote control airplane, Gian loses control of it and it crashes into a river. After Gian flees the scene, Suneo glimpses a massive dinosaur emerge from the water, an encounter that fills him with fear. He tries to tell the others, but their reactions range from disbelief to skepticism, and he ends up seeking help from Doraemon and Nobita, only to be dismissed at first. The tension between ordinary schoolyard worries and extraordinary discoveries begins to blur the lines between imagination and reality.
Nobita and Doraemon then retreat to the hill behind their school, where Doraemon discovers a tunnel using the Anywhere Hole, a portal that promises a way to explore beyond their familiar world. That night, Suneo spots the same dinosaur again in his yard, but this time he questions his own sanity rather than the truth of his sighting. The next day, Nobita leads the group into the tunnel, and Suneo emerges through an exit to witness a herd of dinosaurs, though no one else believes his extraordinary claim. Undeterred, they return to the underground space again, this time with Suneo carrying a camera that later records the crashed airplane, a clue that something extraordinary is unfolding.
Frightened, Suneo darts into a cave, loses his way, and is captured by a knight riding a dinosaur. The others hurry home, as Gian and Nobita’s mothers grow furious, realizing their children have exploited the Anywhere Hole as an excuse to leave home. The hole’s fragility becomes apparent the next day when a truck virtually destroys it, cutting off their underground access. Doraemon apologizes to everyone for the disruption and for Suneo's prolonged absence, but the group remains determined to recover what was lost.
Nobita and Doraemon review the footage from Suneo’s camera and realize that his airplane is still somewhere in that underground world. That night, the friends follow the river to a new entrance into an underworld, where they are briefly captured by native kappas. They are rescued by a knight named Banhou, who reveals that Suneo is in their capital, Enriru. The voyage leads them to the capital city, where they finally locate Suneo. Banhou explains that, once they are permitted to leave, their memories will be erased unless they find a way to preserve them.
As training duties pull at Banhou, his sister Roo offers to guide the group through the underworld, though she warns them not to venture into a forbidden area. The kids visit a museum where they learn that the underworld’s inhabitants believe humans evolved from dinosaurs, and they uncover the mystery behind the dinosaurs’ extinction: something—or someone—has altered the course of history. They also encounter a vast, perfectly rectangular area within the underworld, a clue to the hidden truths of their subterranean home. Roo and many of the inhabitants are unaware that the true sky, Sun, and stars even exist above them.
While riding a dinosaur, Nobita is swept away to the forbidden building, where he stumbles upon a large ship and overhears plans that seek to reclaim Earth’s surface from mammals. He hurries back to warn his friends, and they scramble to flee. In their escape, they are intercepted by kappas again, nearly meeting a deadly end, but Banhou’s ship reappears to rescue them. The vessel, it turns out, is a time machine that launches them into the Cretaceous era, revealing that the underworld’s people had wrongly blamed extraterrestrials for the dinosaurs’ demise.
Nobita and the others race to regroup near the ship, building a camp on a safe ledge. Shizuka notices a comet approaching, adding urgency to their mission. Knights assault their base, while the approaching asteroid—the very event that killed off most dinosaurs—strikes Earth, triggering a colossal tsunami. The knights rush back to the ship, which can shelter them underground, and Doraemon uses a tunnel to shield the group from the rising waters. They realize they have uneasily replicated the large rectangular area from the underworld on the surface—a vast space the size of Hokkaido—before the flood recedes.
When the waters recede, the friends emerge and return to the surface. Doraemon explains the chain of events: the asteroid wiped out a major portion of plants and plankton, forcing herbivores and other dependent species to suffer, while mammals survived by hibernating. The underworld inhabitants conclude that the event must have been an act of God, but Doraemon helps them see the scientific sequence behind extinction and guides them toward creating a lasting underground refuge for the dinosaurs they have saved.
In the end, the main characters are celebrated as heroes. They are allowed to return to the surface with their memories intact, and their belongings that had been left behind underground are restored to them, closing the extraordinary journey with a sense of closure and gratitude for the bond that carried them through the danger and wonder.
