Return of the Joker, as the title suggests, features the return of Batman's arch-nemesis, the Joker, who disappeared some 40 years before the film takes place. Wayne, who knows the reason for the Joker's long absence, is certain that this can't be the same man, and he and Terry set out to discover who he really is and what he's up to. Along the way, it is revealed what happened not only to the Joker, but also to several other Batman-related characters who have been absent from Batman Beyond, such as Batman's old sidekick Tim Drake.
The seemingly immortal Joker has taken control of a faction of the Jokerz, a street gang devoted to the Clown Prince of Crime's image. On his orders, they steal high-tech equipment which Batman had been tracking for weeks. During their latest robbery, the gang escapes, leaving Batman to return to the Batcave.
The next night, Bruce is about to announce his return to active leadership of Wayne Enterprises when the Joker and his cronies interrupt, and the Joker announces his return to Gotham.
Terry seeks answers about his mentor's former nemesis. He first visits Police Commissioner Barbara Gordon, the former Batgirl, but she refuses to tell him anything.