Oceanographer Professor Isabella Garcia-Shapiro and her assistants Baljeet Patel, and Buford Von Stomm, have been assigned to investigate the dissapearance of many ships. Out of a grave twist of fate the group is captured by the visionary yet bitter Captain Phineas Flynn and his first-mate Ferb of the submarine known as the Crustacean. While the group plans to escape, Professor Garcia-Shapiro and Captain Flynn begin to learn from eachother, and fall in love.