The game begins with the Turtles spending their vacation in Key West, Florida. While watching April O'Neil's latest news report, her broadcast is suddenly hijacked by the Turtles' nemesis, Shredder. Taking April as his hostage, Shredder reveals that he has also turned the entire borough of Manhattan into a floating island and challenges the Turtles to come to his lair to stop him.

The game begins with the Turtles spending their vacation in Key West, Florida. While watching April O'Neil's latest news report, her broadcast is suddenly hijacked by the Turtles' nemesis, Shredder. Taking April as his hostage, Shredder reveals that he has also turned the entire borough of Manhattan into a floating island and challenges the Turtles to come to his lair to stop him.