Nobita and his friends discover that Doraemon's gadgets have limits, and the ocean doesn't care. The movie strips away the safety net of infinite futuristic solutions and forces real consequences onto kids just trying to survive underwater. What starts as a summer adventure becomes a test of whether friendship and quick thinking can replace the one thing Doraemon can't provide: a way home when the batteries die.

Doraemon suggests an underwater trip for three days of summer vacation, and Nobita, Shizuka, Suneo and Takeshi head beneath the sea. Jaian and Suneo take Doraemon's underwater vehicle in search of a treasure ship, but the device keeping them safe begins to run out of power, leaving them exposed to the ocean. Marine creatures rescue them, and the group is later captured by these beings, who turn out to live in Mu, an undersea kingdom that has shunned the surface for thousands of years. A greater danger looms: Atlantis, another sunken kingdom now run by robots, has mistaken a volcanic eruption for an invasion and is ready to destroy Earth with nuclear weapons. Aided by a young boy from Mu, Nobita and his friends set out to stop the robots.