Jack Thompson is a pilot of an American B-17 bomber during World War II. His plane is shot down by German fighters and is about to crash. However, a mysterious portal appears, transporting Jack into an alternate reality. Jack ends up in a jungle and promptly saves a young woman who is attacked by a gigantic dinosaur. It appears that the woman is a princess who was about to be sacrificed for her father. The two decide to travel together, trying to survive in the dangerous jungle and eventually escape.

Bermuda Syndrome is a cinematic platformer similar in concept to Flashback. The emphasis of the gameplay is on solving problems and carefully proceeding through screens filled with enemies and hazards. Jumping, fighting, and occasionally using items are required to succeed. At some points it is necessary to interact with the princess in order to solve a puzzle.