Upon hearing about the story of Treasure Island, Nobita dreams of discovering and exploring his own treasure island, despite the fact all of the Earth has been mapped already. Doraemon provides Nobita a special treasure map that shows him the location of a treasure island. At the same time, the media announces the discovery of a completely unknown island. Believing the new island is the treasure island, Nobita recruits Doraemon and Shizuka to journey with him, with Doraemon providing a ship. Gian and Suneo also tag along. However, as they get near the island, they are suddenly attacked by a gang of pirates. At that moment, the island begins to move, revealing that it is, in fact, part of a massive, highly advanced ship. The pirates retreat but abduct Shizuka in the process. Nobita and his friends are unable to rescue her, but save an unconscious boy named Flock.

Flock explains that the pirates that attacked them are in fact time travelers who travel to different eras to steal treasure off the sea floor, and he himself was part of the ship's crew but decided to desert since he couldn't accept taking orders from Captain Silver. Doraemon uses the treasure map to track the pirate ship's location. Meanwhile, on the pirate ship, Shizuka encounters Sarah, Flock's sister. Sarah agrees to help Shizuka. Both Flock and Sarah reveal that Captain Silver is, in fact, their father, who went mad when their mother died and has become obsessed with gathering as much treasure as possible. Nobita and his friends attempt a rescue operation, but end up rescuing picking up Sarah instead of Shizuka, who is taken directly to Captain Silver.

Captain Silver then moves on the final stage of his plan. Having seen humanity's destruction in the future, he is determined to launch his pirate ship into space and colonize a new planet with all of the treasure he has acquired. However, this requires him to drain the Earth's energy to get the power he needs to reach space. Doraemon warns that taking Earth's energy will result in its destruction so Nobita, his friends, Flock, and Sarah attack the pirate ship again. Gian and Suneo stay behind to occupy the pirates while Nobita, Doraemon, Flock, and Sarah confront Captain Silver directly. While Nobita and Doraemon delay the activation of the pirate ship's engine, Flock is able to seize control of the ship and eject the energy back into Earth. Captain Silver comes to realize how badly he had neglected his children, and abandons his plans, promising to be a better father to them. Afterwards, Flock, Sarah, Captain Silver, and the rest of the crew return to their own time while Nobita and his friends return home, with Nobita gaining a new appreciation for his own father.