The film opens with a group of pirates searching an island for treasure who are then all captured, it then cuts to Nobita and his friends discussing about a school project themed around seas and oceans. Interested in pirate life and treasury, Nobita asks Doraemon to help him find secret treasures. Doraemon at first reject hims outright thinking it is ludicrous, but after learning news about recently discovered treasury, he helps Nobita in his sea voyage in search for the secret treasure. Bringing along Shizuka, Gian, and Suneo, they roam the Pacific Ocean while playing ship and sea danger simulators with Doraemon's gadgets.

However, Doraemon senses a time distortion that takes the group to the 16th century, where real dangerous phenomena and sea monsters begin appearing. When a whirlpool destroys the group's ship, Nobita goes missing after failing to hold on, while the others are rescued by 16th century-pirates boarding a huge pirate ship. All but a few of Doraemon's gadgets are gone following the whirlpool incident and they must assist the pirates in rescuing their comrades, with a female pirate named Betty having lost track of her brother and father and Captain Kidd, who is the leader of the company. Although Doraemon's treasure map is torn in half, the pirates learn that their map is exactly the same as their own treasure map, confirming the existence of the secret treasures.

Meanwhile, Nobita is rescued by a dolphin and taken to an island where Betty's younger brother, Jack lives. Although Nobita is unable to converse with Jack due to a language barrier, the two befriend and Nobita learns the dolphin's name, Ruffin, as well as the fact that Jack is also separated from his family, like himself. The pirate company eventually arrives at the island and begins searching for Nobita and Jack. One by one, the pirates and Doraemon's company are attacked and captured by strange creatures and security guards, eventually all but two of the pirates are captured.

After Rufin catches a glimpse of the other torn half of treasure map owned by Nobita, it quickly leads Nobita and Jack to a 22nd-century-underground facility, but are captured by security guards. It is revealed that the facility is run by a 22nd-century businessman named Cash, who creates and sells genetically altered animals for money with the help of a scientist, Dr. Clone. Ruffin is taken to be experimented in Dr. Clone's laboratory, while Nobita and Jack are thrown to jail and reunited with Doraemon and the pirate company.

The uncaptured pirates then bail all the others as well as the pirates captured at the start of the film, including Betty and Jack's father, out. Nobita and his friends go to break the control system and free Ruffin. Cash orders the genetically altered animals to attack the company, but they manage to defeat all of them. Eventually, Cash's masterpiece, a sea monster named "Leviathan" attacks the group. The sea monster swallows Doraemon and Cash, but the former manages to get himself and Cash out through the Dream Checking Machine. The sea monster crashes into the walls of the cave which contains the facility which caves in, effectively flooding it.

As the island starts sinking, the company escapes from the island with the help of Ruffin and its other dolphin friends. Cash and his company are arrested by the Time Patrol summoned by Ruffin, who is revealed to be a secret agent of them who was sent to bust out Cash and his associates. The pirates, having recovered their leader, the pirates are now rich as they have found the secret treasures on the island.

The film ends with Nobita and his friends bidding farwell, returning to the present time but not before seeing the pirates erecting a sail featuring Doraemon's face on it, by saying "Goodbye Captain Doremon".

The film was released in the theatres of Japan on 7 March 1998.

• Doraemon The Movie 25th page (in Japanese)
• Doraemon: Nobita's Great Adventure in the South Seas at IMDb