Johnny Gray is the engineer for the Western and Atlantic Flyer, and his engine is named "The General." There are two loves in Johnny's life, "The General" and Annabelle Lee. During a visit to Annabelle's home, her brother comes in and announces that Fort Sumter has been fired upon, and, immediately, he and Annabelle's father go to enlist in the Southern cause. Johnny does, too, but he is rejected because "he is more valuable to the South as an engineer." Due to a misunderstanding, Annabelle's father and brother think Johnny refused to sign up. After being told of his supposed cowardice, Annabelle informs Johnny that she will not speak to him again until he is in uniform. A year later, a group of Union soldiers led by Captain Anderson steal Johnny's train with Annabelle in one of the boxcars. Johnny gives chase in another train with all sorts of mishaps and comicals events happening along the way. Deep into Union territory, the Yankee soldiers realize Johnny is alone on the train. Johnny deserts the train and flees into the woods.

Heading for a newly inherited island, the boys are shipwrecked and marooned on an atoll which has just emerged from the sea. Along with their cook, a stowaway and a girl who is fleeing her fiancé, they set up their own government on the atoll. Uranium is discovered and world powers begin fighting over ownership of the island.