Dekisugi (voiced by Sumiko Shirakawa), Gian (voiced by Kazuya Tatekabe), Nobita Nobi (voiced by Noriko Ohara), and Shizuka Minamoto (voiced by Michiko Nomura) begin by watching a televised report about a mysterious disappearance of a herd of flamingos, a news item that seeds Nobita’s dream of flying. Nobita, inspired and restless, fashions wooden wings after Doraemon, Nobuyo Oyama, refuses to help him learn to fly; his initial attempts fail, leaving him determined to find another way to soar. While he and Shizuka help her canary reclaim its freedom, a bright portal slices across the sky and a humanoid bird rides in on an airplane, stepping into their world with a calm, curious air.
That stranger introduces himself as Gusuke, Bin Shimada, a resident of the distant world Birdopia. Doraemon, Nobita, and Shizuka quickly strike up a friendship with him, drawn by his warmth and the promise of companionship in a place so unlike their own. When Gusuke departs to return home, Gian and Suneo Honegawa, Kaneta Kimotsuki, snatch his airplane, prompting the trio to chase after through the interdimensional portal.
They arrive in Birdopia, where Gian and Suneo are swiftly captured by crow soldiers and brought before the vulture commander Seagrid, who harbors a deep grievance against humanity. Back in the human world, Doraemon, Nobita, and Shizuka locate Gusuke near the owl Professor Hou’s house after fleeing the same guards, aided by a quirky ostrich taxi service. Professor Hou, Ichiro Nagai, explains that Birdopia exists far from the human world and is connected to Earth only during bird migrations, a connection safeguarded by the Bird Migration Patrol Troops. Seagrid, who once served the patrol, retired after being wounded by humans and now seeks vengeance. He and his followers are determined to seize Phoenicia, a legendary force the group discovers could annihilate humanity if awakened.
Hou advises the friends to hide, and Doraemon introduces “Bird Hats”—special headgear that can sprout wings, turning Doraemon into a pigeon, Nobita into a duck, and Shizuka into a swan. With the help of Gusuke, the trio stages a daring rescue of Gian and Suneo, and Doraemon provides them with Bird Hats shaped like an albatross and a woodpecker. Gusuke reveals a troubling truth: he is adopted, and his inability to fly stems from a trauma he suffered just before he was found. The conversation deepens the emotional stakes, revealing the personal costs behind his dream of flight.
Meanwhile, Hou uncovers an ancient tablet that details Phoenicia, a dragon-like being with the power to destroy worlds. Seagrid learns of this discovery and kidnaps Hou to force the location of Phoenicia from him. The narrative threads converge at the Rally Icarus, an annual event designed to recruit new members for the Patrol Troops. Gusuke wins the rally but is disqualified when Seagrid’s falcon lieutenant Babylon—acting on Seagrid’s orders—claims that those who fly with machines are disqualified. The group soon discovers that Hou has gone missing, and Doraemon, after reading the tablet with Translator Jelly, realizes they must find Icarus, a legendary eagle imprisoned in Birdopia’s prison after being accused of aiding Seagrid’s capture of Seagrid’s ally.
United by a common goal, they persuade Icarus to help stop Seagrid from awakening Phoenicia, which lies buried atop an icy mountain. Along the way, they stumble upon a projector that reveals a hologram of Mamoru Torino, a 23rd-century ornithologist obsessed with creating a safe haven for birds, a figure tied to the origins of Birdopia. Despite their efforts, Seagrid awakens Phoenicia, a catastrophe that dwarfs previous threats. Doraemon fights to de-evolve Phoenicia into a simple amoeba using his Transgression Beam, but a clash with Babylon diverts the beam, mutating Phoenicia into a larger, more formidable creature.
Phoenicia’s rampage tests everyone’s resolve, and Seagrid’s ambitions nearly bring him to ruin before Icarus intervenes to save him. Gusuke earns his wings in a pivotal moment, gaining the courage to fly as Icarus, who is revealed to be his father in a beam of cinematic drama, passes on the gift that lets him rise to the challenge. Gusuke lures Phoenicia toward the Perched Tree, while Doraemon and Nobita ascend to the tree’s summit to reach Mamoru Torino’s time machine, hoping to neutralize the threat. When their attempt fails, Doraemon transports both the machine and Phoenicia back to the Pre-Hadean Era, bending the course of time to avert catastrophe.
In the aftermath, Birdopia and its inhabitants celebrate their hard-won peace, and the human friends bid a heartfelt farewell to their new allies. Nobita and Shizuka return to their world with the rest of their companions, and Shizuka also brings back her devoted canary. The bond between worlds endures, and the film closes on a note of friendship, resilience, and the quiet power of courage found in the most unexpected places.