Nobita Megumi Oohara dreams of discovering and exploring his own Treasure Island, even though the Earth has already been mapped in full. Doraemon Wasabi Mizuta presents a special treasure map that seems to point toward a hidden paradise, and at the same time the headlines announce the discovery of a completely unknown island. Believing this might be the long-sought treasure island, Nobita teams up with Shizuka Yumi Kakazu and is joined by Gian, Subaru Kimura, and Suneo, Tomokazu Seki, with Doraemon supplying a ship for the journey.
As the group approaches, a gang of pirates attacks, but the island unexpectedly begins to move, revealing that it is actually part of a colossal, advanced ship. The pirates retreat, yet they abduct Shizuka in the confusion. Nobita and his friends manage to rescue an unconscious boy named Flock, who explains that the pirates are time travelers—they hop between eras to steal treasures from the seas. Flock reveals that he used to be part of the ship’s crew but deserted because he could not accept taking orders from Captain Silver. Doraemon uses the treasure map to track the pirate vessel and its unusual quarry.
On the pirate ship, Shizuka meets Flock’s sister Sarah, who looks exactly like her. Sarah agrees to help Shizuka, and the two reveal that Captain Silver is actually their father, a man who lost his grip after their mother’s death and has become obsessed with gathering as much treasure as possible. Nobita and his friends mount a rescue operation, but in a twist they end up saving Sarah instead, while Shizuka is taken directly to Captain Silver. The pirate captain unveils a shocking plan: he intends to launch his ship into space to colonize a new planet, and to do so he needs to drain Earth’s energy. Doraemon warns that sapping Earth’s power would destroy the planet.
A renewed assault follows, with Nobita, Doraemon, Flock, and Sarah taking on the pirate ship once more while Gian and Suneo stay behind to keep the pirates occupied. The climactic confrontation with Captain Silver unfolds as they delay the engine and wrest control of the ship. Flock manages to eject the ship’s energy back toward Earth, thwarting the catastrophic move. Realizing the cost of his fixation on treasure and the pain it caused his family, Captain Silver relinquishes his destructive plan and vows to be a better father to his children.
With the danger passed, the crew returns to their own time. Nobita and his friends head home, and Nobita gains a new, deeper appreciation for his father, Nobisuke Yasunori Matsumoto. The adventure leaves a lasting impression: sometimes the real treasure lies not in gold or gadgets, but in family, responsibility, and the choices that shape the people we become.