The film opens with Dekisugi, Gian, Nobita Nobi, and Shizuka Minamoto watching a televised report about a herd of flamingos mysteriously disappearing. After the footage airs, Nobita dreams of flying and, feeling determined, builds wooden wings when Doraemon refuses to help him, resulting in a string of failed attempts to take to the sky. The tension shifts as a new spectacle unfolds: a portal splits open in the clouds and a humanoid bird riding an airplane steps through, catching everyone by surprise.
He introduces himself as Gusuke, a humanoid bird who lives in a distant world called Birdopia. Doraemon, Nobita, and Shizuka step in to help Gusuke repair his aircraft, and a fast friendship blossoms. When Gusuke departs to return home, Gian and Suneo catch sight of him and seize his plane, prompting the others to chase after them through the portal into this strange, feathered realm.
Arriving in Birdopia, Gian and Suneo are swiftly captured by crow soldiers and brought before the vulture Commander Seagrid, who harbors plans of execution. Meanwhile, Doraemon, Nobita, and Shizuka find Gusuke near Owl Professor Hou’s house after fleeing the same captors with the aid of an ostrich taxi. Hou explains that Birdopia is a world far from the human one, connected only during bird migrations and guarded by the Bird Migration Patrol Troops. Seagrid—the fallen former member of those troops—has turned to vengeance after being wounded by humans. He dreams of shaping Birdopia in his own image and seeks to awaken Phoenicia, a power that could spell doom for humanity.
To survive, the group hides as Hou advises, and Doraemon brings special “Bird Hats” that sprout wings when worn, turning him into a pigeon, Nobita into a duck, and Shizuka into a swan. Through courage and teamwork, the trio and Gusuke stage a daring rescue of Gian and Suneo, and Doraemon outfits them with new Bird Hats modeled on an albatross and a woodpecker, respectively.
Gusuke reveals that there will be an annual event called the Rally Icarus, a recruitment rite for the Patrol Troops, and urges Nobita and friends to join and prove themselves. During a dinner with Gusuke’s adoptive family and his friend Milk, Gusuke confesses that he is adopted and cannot fly naturally because of trauma from a past fall, which weighs on him deeply.
Meanwhile, Hou deciphers an ancient tablet that hints at Phoenicia, a dragon-like ancient being capable of destroying the world. The crow captain reports this to Seagrid, who then abducts Hou to locate Phoenicia and fulfill his plan to destroy humanity.
At the Rally Icarus, Gusuke wins the competition but is disqualified when Babylon, Seagrid’s falcon lieutenant, enforces a rule against those who rely on machines to fly. The group learns Hou is missing; Doraemon uses Translator Jelly to read the tablet and identify Icarus, a legendary eagle imprisoned in Birdopia’s prison after being wrongly blamed for Seagrid’s shooting. They set out to find him, hoping his wisdom and strength can halt Seagrid’s scheme.
The mission leads them to a crucial discovery: Icarus agrees to help stop Seagrid from awakening Phoenicia, a mission that takes them to a frozen mountain where Phoenicia lies dormant. Along the way, a mysterious projector reveals a hologram of Mamoru Torino, a 23rd-century ornithologist who once pursued a dream of creating a safe haven for birds, a dream that helped build Birdopia. Yet the group arrives too late—the alarm has already been sounded and Phoenicia is waking.
Doraemon attempts to de-evolve Phoenicia into an amoeba using his Transgression Beam, but a scuffle with Babylon results in the beam misfiring and instead evolving Phoenicia into a larger, more formidable form. Phoenicia’s rampage tests everyone’s resolve, but Icarus unexpectedly lends Gusuke the courage he needs to fly. Gusuke discovers his own power and uses it to lure Phoenicia toward the Perched Tree, where the final confrontation looms. Doraemon and Nobita ascend to the tree’s summit, determined to reach Mamoru Torino’s time machine and neutralize Phoenicia once and for all. When the plan falters, Doraemon seizes a bold option: he uses the time machine to cast Phoenicia back to billions of years in the past, to the Pre-Hadean Era.
With Phoenicia contained and the damage repaired, the people of Birdopia celebrate together. The friends bid their farewells to their feathered hosts, and Shizuka returns home with her cherished canary, while Nobita and the others return to their own world, carrying the memories of a voyage that bridged two very different realms.
