A heroic version of Lex Luthor from an alternate universe appears to recruit the Justice League to help save his Earth from the Crime Syndicate, an evil version of the League. What ensues is the ultimate battle of good versus evil in a war that threatens both planets and, through a devious plan launched by Batman's counterpart Owlman, puts the balance of all existence in peril.

The gang goes on a trip to check on Velma's younger sister, Madelyn. She's been studying stage magic at the Whirlen Merlin Magic Academy, where apparently there have been sightings of a giant griffin. The gang decides to investigate.