With the Justice League's sudden disappearance, Lois Lane and Jimmy Olson investigate the Hall of Justice but are quickly chased out by a phantom, prompting them to call Mystery Incorporated for help. En route to Metropolis, the gang discover that the city is overrun by super-villains as a result of the missing Justice League. After barely managing to escape to the Daily Planet, they meet up with Lois and Jimmy (who proclaims Daphne as his girlfriend, despite her protests) who explain the phantom situation. As the gang tour the Hall of Justice, they meet Lex Luthor, Mercy Graves, and Luthor's dog, Rex. Mystery Incorporated teams up with Krypto the super-dog to investigate the disappearance of the Justice League.