The plot revolves around a summer vacation of Nobita and his friends under the waters of Pacific Ocean. Jaian and Suneo take Doraemon's underwater vehicle and travel through the Atlantic Ocean, trying to find a treasure ship.

Along the way, they discover that the environment gun that Doraemon used to protect them is running out of energy leaving them vulnerable to the sea. Fortunately, they are rescued by some marine creatures.

Doraemon and his friends are later captured by these creatures, revealed to be inhabinats of the underwater kingdom of Mu. It is revealed that another undersea kingdom, Atlantis, now controlled by robots, was about to destroy the Earth with nuclear weapons after mistaking a volcano eruption for an invasion.

With the help of a young boy from Mu, Nobita and his friends attempt to stop the robots, but are all captured. However, when things are at their grimmest, Doraemon's robotic underwater vehicle sacrifices itself to destroy the computer that controlled all the robots and nuclear weapons.

After returning to Mu, Doraemon and his friends are hailed as heroes.