An opening scene follows a boy from a prehistoric era who hunts a fish, returns to his ruined village, and is suddenly sucked into a time vortex that hurls him into 20th‑century Japan.
In that modern world, Nobita longs to run away from home and starts by trying to set up a makeshift living space, though persistent land ownership rules keep blocking his progress. Meanwhile, his friends Shizuka, Gian, Suneo, and Doraemon also want to escape their families. Nobita proposes a radical plan: travel back in time to a place in Japan that is free of human habitation. The group agrees, and they journey to prehistoric Japan, roughly 70,000 years in the past.
Once there, Doraemon assigns each member a ministry to oversee in this untamed world: Shizuka heads the Ministry of Gardening, Gian runs the Ministry of Development, Suneo leads the Ministry of Agriculture, and Nobita governs the Ministry of Pets, with Doraemon supervising all of them. Nobita then experiments with gene tinkering and creates a dragon, a griffin, and a pegasus—named [Draco], [Gri], and [Pega]—which he hides from Doraemon as the others watch with a mix of awe and concern.
That night, the group shares a meal and contemplates a return home, planning to revisit this time again later. The next day, a boy from the prehistoric world slips into Nobita’s room and hides in the closet. When Gian and Suneo arrive, the boy attacks Gian, who fights back until the intruder collapses from exhaustion. Nobita, Shizuka, and Doraemon arrive to aid, and the two groups retreat to a cave where Shizuka tends to the injured visitor.
Doraemon uses a time-signal to locate the boy’s origin in present-day China, a land already inhabited by humans in this era, and a translation device helps them understand him. The visitor explains he belongs to the Light Tribe, whose people were attacked by the Dark Tribe. The friends decide to help, and they set off on a journey to trace the Dark Tribe on their magical mounts—the Pegasus, the dragon, and the griffin—for four days. On the fourth day they locate and clash with the Dark Tribe, but a magical dogū puppet proves powerful and poses a serious challenge, briefly overwhelming them despite Doraemon’s gadgets.
Unknown to them, the dogū has a way to restore itself after the group departs. The team brings the Light Tribe to a peaceful spot in Japan to live, and then returns home for the night. The next day Doraemon reveals that the dogū’s self-restoration endangers the Light Tribe once more, so they travel back to the past to intervene again. Arriving back, they find that the Light Tribe’s village has already been destroyed by the Dark Tribe, and Nobita becomes separated from the others in a brutal snowstorm.
With the others continuing their search, they locate the Light Tribe and confront Gigazombie—the king of spirits and a time-criminal from the 23rd century who seeks to rewrite reality by destroying time itself. He easily defeats Doraemon and the others because his gadgets are more advanced. Meanwhile, Nobita discovers a mysterious box containing a mammoth figure that urges him to press a button if he needs help. Nobita’s loyal companions—the Pegasus, Draco and Gri—return to aid their friend, but Gigazombie traps them in a desolate corner. Nobita presses the button, and the Time Patrol arrives to arrest Gigazombie.
With Gigazombie detained, the creatures Pegasus, Draco, and Gri are transported to the future, revealing they were never meant to exist in the present era. The friends share a sad farewell and finally return home, richer for the journey and the bonds they forged across time.
