Nobita discovers a fossilized dinosaur egg during a museum excavation. Using Doraemon's Time Cloth, he restores and successfully hatches the egg, revealing twin feathered dinosaurs of an unknown species absent from future encyclopedias. He names them Kyu and Myu based on their distinct vocalizations. Nobita assumes primary responsibility for their care, learning nurturing techniques from a dinosaur expert. He diligently feeds them, initially houses them in his room, and later provides expanded space using the Breeding Diorama Set gadget. This role demonstrates his capacity for responsibility when invested in another being's wellbeing.

The dinosaurs exhibit contrasting traits: Myu masters gliding and integrates easily, while Kyu struggles due to a shorter tail and inability to glide, mirroring Nobita's perceived shortcomings. Nobita forms a particularly strong bond with Kyu, relating to his difficulties. When the dinosaurs outgrow the modern era, Nobita makes the difficult decision to return them to their original time. He, alongside Doraemon and friends, travels back to the Late Cretaceous via time machine intending to locate Kyu and Myu's species.

During the time-travel expedition, the group confronts prehistoric dangers and discovers they accidentally arrived in the Jurassic period. They lose the Breeding Diorama Set in a swamp. Nobita perseveres in searching for a suitable habitat for Kyu and Myu, encountering dinosaurs like the Tarbosaurus Cole and the Sinoceratops Top. Using Tomodachi Chocolate, these initially threatening dinosaurs become allies. The journey is complicated by the covert surveillance of Time Patrol agents Jill and Natalie.

The group eventually locates an island populated by dinosaurs identical to Kyu and Myu, later revealed to be the lost Breeding Diorama Set enlarged over time. Upon introduction, the resident herd rejects Kyu due to his inability to glide, physically wounding him. Witnessing this, Nobita passionately defends Kyu, declaring he will prove Kyu can fly beautifully. Concurrently, they realize they are in the timeframe of the Cretaceous-Paleogene extinction event. Facing the imminent meteor impact, the Time Patrol initially intervenes to prevent interference. Nobita, determined to save the dinosaurs, defies them, attempting to use the "Opposite Direction" gadget to divert the meteor. His protective stance over Kyu and Myu when detained, and a subsequent check by Jill using a "check card" that emits light, leads the Time Patrol to cease interference.

Nobita participates in a rescue operation to save the dinosaurs from extinction. Using the Spatial Movement Crayon, they relocate dinosaurs onto the enlarged Breeding Diorama Set island and activate its weather control function to shield them from the meteor's aftermath. During this critical task, a large pterosaur attacks Nobita. Kyu, witnessing Nobita in peril, achieves powered flight through determined flapping, evolving beyond gliding. He rescues Nobita mid-fall. This act represents a key evolutionary step from dinosaurs to birds, observed by the Time Patrol. After ensuring the dinosaurs' safety on the island, Nobita bids an emotional farewell to Kyu and Myu. Upon returning to his time, Nobita successfully performs a horizontal bar exercise he previously failed, demonstrating newfound perseverance and self-reliance achieved without gadget reliance, mirroring Kyu's achievement.