The world's first atomic powered sub is about to be launched when it disappears in front of everyone. Secret Squirrel hears about it on the radio and reports to headquarters. The Chief tells him that he must return the sub intact and hurry, the fate of the world is at stake.
Secret Squirrel and Morocco Mole take a boat out into the ocean and Secret uses a magnet to find the submarine. It seems that the evil Captain Ahab was the one behind the disappearance and he shows off how he did it by making it disappear again. He knocks Secret off the sub.
Secret tells Captain Ahab to surrender and the captain laughs at him. Secret fires several rounds out of his rapid fire bazooka and the captain uses a device to return all of them sinking the boat that Secret and Morocco were one.
Captain Ahab captures Secret and Morocco and has them tied to the periscope. He tells them that he plans to destroy the world with a missile. He goes to fire it as Secret pulls out some scissors from under his hat and cuts the ropes. Secret leaves the sub and goes to catch the missile and returns it to the captain in the sub and blows it up.
Secret reports to the Chief and the Chief asks what happened to the sub. Secret shows him the pile of parts outside the window and he and Morocco are going over the instructions on how to put it back together.