Lieutenant Crash Corrigan, in his last year at Annapolis, is invited by Billy Norton to visit his father, Professor Norton, after a wrestling match. At their house, the professor is demonstrating his new invention, which can detect and prevent (at short range) Earthquakes, to Diana Compton and his theory about regular tremours from the area where Atlantis used to be.
When Atlantean tyrant, Unga Khan, and his Black Robe army turn their Disintegrator beam on St Clair, Professor Norton leads an expedition to investigate. Along with him in his Rocket Submarine are Crash, Diana, three sailors (Briny Deep, Salty, Joe) and their pet parrot Sinbad. Unknown to the expedition until it is underway and in trouble, Billy has stowed away on the Rocket Sub as well.
Problems for the expedition begin when Joe, in charge of the engine room, is driven mad by the fear that the submarine cannot survive such depths. In order to prove this, he locks the engine room door and sends the sub into a fatal dive. As soon as this crisis is averted, Unga Khan and Captain Hakur detect their approach and bring them through a tunnel into the Inland Sea with a Magnetic Ray.