In the Neo-Gotham City, the Joker resurfaces after having disappeared 40 years earlier. He has taken over a faction of the Jokerz, and on his orders, they steal high-tech communications equipment. One heist happens to coincide with Bruce Wayne's formal announcement of his return to active leadership of Wayne Enterprises, revealing the Joker to the world. Despite Terry McGinnis' intervention, the Joker escapes. Bruce insists that it must be an impostor, as he claims to have witnessed the Joker's death decades before, yet all evidence suggests otherwise. Bruce, unwilling to let Terry face the Joker, impostor or not, demands that he return the Batsuit, to which Terry reluctantly complies.

Later on, Terry is attacked by the Jokerz at a nightclub he is at with his girlfriend, Dana. At the same time, the Joker ambushes and attacks Bruce in the Batcave, leaving him for dead. Terry defeats the Jokerz, and Dana is taken to the hospital for her injuries. Terry rushes to Wayne Manor, and finds Bruce near-dead from Joker venom. Terry quickly administers an antidote, and tends to Bruce with the help of Barbara Gordon.

After Terry insists on being let in on what really happened to the Joker, Barbara reluctantly tells him that many years back after Nightwing (Dick Grayson) moved to a new city to fight crime on his own, the Joker and Harley Quinn kidnapped Tim Drake, the third Robin, and disfigured him to look like the Joker, and tortured him to the point of insanity. In the process, Tim revealed Batman's secret identity—and the secret of what drives him to be Batman. When Batman and the Joker fought their final battle, the Joker got the upper hand and subdued Batman. The Joker then tried to get Tim to kill Batman, but the boy instead turned on the Joker and kills him, to which Tim suffers a mental breakdown and starts crying as young Barbara Gordon (then known as Batgirl) comforts him. Batman and Barbara buried the Joker's body beneath Arkham Asylum, while Harley fell into a pit after she was fighting Batgirl and was never found but she is presumed dead. Following the incident, Tim was rehabilitated, but Bruce forbade him from being Robin again. Barbara retired as Batgirl to become police commissioner, and Tim eventually settled down with a wife and family, and a career as a communications engineer.

Terry decides to question Tim, who denies any involvement and bitterly says he had grown sick of his past life as Robin. Terry then suspects Jordan Price, who would have taken control of the company were it not for Bruce's return. Jordan Price, thinking he will become CEO, plans to hold a private party on his yacht with his girlfriend Amy. However he finds Dee-Dee in her place, Amy having been tied to a pole and gagged at the port. Terry finds the Jokerz on Price's yacht, who reveal that Price had hired them and given them access codes. However, the Joker has sent them to kill Price, as he is no longer needed. Terry rescues Price before a satellite laser destroys the boat, and then turns him in to the police with a recording of the conversation.

Back in the Batcave, Terry deduces that Tim must be working with the Joker when he discovers that the high-tech equipment the Jokerz have been stealing can be combined to form a machine that takes control of any satellite, thus explaining what happened on the yacht—and it can only be built by an engineer of Tim's caliber. Bruce is skeptical, but nonetheless sends Terry to question Tim again. Terry tries to confront Tim, but is lured into a trap by the Joker, who confirms that he and Tim are indeed working together. Escaping in the Batmobile, he is then chased through Gotham by the laser-armed satellite.

Terry tracks the Joker to the abandoned Jolly Jack candy factory. After fighting off the Jokerz, he finds Tim, who transforms into the Joker before his eyes. The Joker explains that when he kidnapped Tim, he implanted a microchip in the boy that carries the Joker's consciousness and personality, allowing him to physically and mentally transform Tim into a clone of himself. The Joker prepares to fire the satellite again to kill Dana, Terry's family and Bruce, but before he can, Terry sets Bruce's dog, Ace, on him. Terry knocks the Joker's joy buzzer into the controls, destroying the beam's guidance system, causing it to head to the factory.

The Joker attempts to escape, but Terry seals the factory. A fight ensues between the two, but the Joker is easily able to overcome Terry since he knows all of the original Batman's moves and tricks. Terry then decides to improvise by using his expertise in dirty street fighting moves and mocking his obsession with Batman. An agitated Joker throws a handful of grenades at Terry, sending him crashing to the floor. The Joker then pins him to the ground and begins to strangle him. Terry, having covertly retrieved the Joker's joy buzzer, delivers a shock to the Joker's neck, destroying the chip, reverting Tim to his old self, and destroying the Joker forever. Terry escapes with Tim and Ace before the satellite destroys the factory. The satellite gets deactivated and floats into outer space.

In the city jail, two of the female Jokerz, Deidre and Delia Dennis, are bailed out by their grandmother, an elderly Harley Quinn, who laments what disappointments they are. Meanwhile, Terry and Barbara meet Tim in the hospital. Bruce arrives just as Terry leaves, telling him that it is not being Batman that makes him a worthwhile person, but the other way around. Bruce then joins Barbara and Tim in the hospital room. The film ends with Terry donning the Batsuit and flying off into the heart of the city.

• Will Friedle as Terry McGinnis / Future Batman
• Kevin Conroy as Bruce Wayne / Original Batman (young)
• Mark Hamill as The Joker and Jordan Price
• Angie Harmon as Commissioner Barbara Gordon
• Dean Stockwell as Tim Drake
• Teri Garr as Mary McGinnis
• Arleen Sorkin as Dr. Harleen Quinzel / Harley Quinn and Amy Price
• Tara Strong as Barbara Gordon / Batgirl (young)
• Mathew Valencia as Tim Drake / Robin (young)
• Melissa Joan Hart as Delia & Deidre Dennis / Dee-Dee
• Don Harvey as Charles Buntz / Chucko
• Michael Rosenbaum as Stewart Carter Winthrop III / Ghoul
• Frank Welker as Woof the Hyena-Man, Ace the Bat-Hound
• Henry Rollins as Benjamin Knox / Bonk
• Rachael Leigh Cook as Chelsea Cunningham
• Lauren Tom as Dana Tan
• Vernee Watson-Johnson as Ms. Joyce Carr
• Mary Scheer as Mrs. Drake
• Jason Stanford as Gangster

• Both Jordan Pryce and the Joker were played by Mark Hamill. This furthered the idea of Pryce being a red-herring, as the character not only resembled the Joker, but shared his voice actor. The same idea was done in Batman: Mask of the Phantasm.
• Ghoul was played by voice-actor Michael Rosenbaum, who did several voice-acting characters for the Batman Beyond TV series as well as playing the Flash in Justice League and playing Lex Luthor on Smallville. While in the recording studio, he would often do a Christopher Walken impression; when they were commissioned to create this film, they modeled the character on Rosenbaum's Walken impression.
• Although Harley Quinn was originally set to be killed in the flashback sequence, a short scene near the end of the movie just after the climax features an older woman who resembles Harley releasing her twin granddaughters, Delia and Deidre Dennis. When the old woman scolds the two twins, one of them replies: "Shut up, Nana Harley!" Dini included this scene in the script because of his displeasure at being asked to kill off what he felt was one of his biggest contributions to the Batman mythos; Timm chose to retain it because he felt it provided some necessary comic relief.
• Upon being shot, Bonk's corpse was set to be seen throughout the rest of the scene in the background twitching, but the producers were asked to leave it out early in the film's development.
• In the "Our Family Memories" video, Joker's apron was originally going to say "Kill the Cook", rather than the final's "Kiss the Cook".
• Also in the "Our Family Memories" video, the table was supposed to have surgical tools rather than the final's bagels, plungers, and cream cheese.
• Paul Dini makes a cameo during the first few minutes of the movie.
• Joker's hideout, the Jolly Jack Candy Factory, is reference to Jack Kirby, who during his early Marvel Comics days was known as 'Jolly' Jack Kirby.

• The Joker's remains have appeared in the Batman Beyond episode "Joyride" which the Jokerz used for their initiation ritual. A deleted scene in the movie would have involved Bruce Wayne checking on these remains to ascertain whether or not the original Joker was really dead. Wayne finds the body suspended over the Arkham Operating Theatre with a note pinned to the chest reading "I know".
• Enhanced versions of the Jokerz seen in Return of the Joker later appear in the Justice League Unlimited episode "The Once and Future Thing: Part II—Time Warped" thanks to the actions of supervillain Chronos. In this episode, Terry is killed by the Jokerz but Green Lantern and the original Batman manage to subdue Chronos and put things right, therefore restoring Terry and returning the Jokerz to normal.
• Continuity-wise, Return of the Joker appears to be set after the Batman Beyond episode "King's Ransom" where Paxton Powers is arrested, therefore leaving Wayne-Powers up for grabs. But it would be fair to assume the film takes place after the entire series as none of the plot elements get followed up as no mention is made of the Joker or Tim Drake during the third season until the Static Shock episode "Future Shock" and the Justice League Unlimited episode "Epilogue". Producer Bruce Timm has reportedly stated that the events in said flashback take place at the end of the current DCAU timeline which is after the Justice League Unlimited series finale "Destroyer" but before the Batman Beyond series premiere "Rebirth" but Batman, Batgirl, Robin and Harley Quinn retain their The New Batman Adventures designs while the Joker appears in his Static Shock and Justice League design. However, this is most likely because this movie was released and the Joker's design was first created before it was used for Static Shock and the Justice League series later on.
• In the Justice League Unlimited episode "Epilogue", it was revealed that the genetics technology used by the Joker had been stolen from Project Cadmus.

The movie was initially released amid the backlash against violence in movies and video games aimed at children that followed the Columbine High School massacre of 1999; as a result, the movie was substantially re-edited shortly before release to tone down the violence. Many of the changes were controversial, particularly those made to a key scene in which the Joker is killed. The original unedited version has been released as "The Original Uncut Version."

The following are scenes that were changed in the edited-for-content (Unrated) version:

• In general, references to death and killing are removed from character dialogue, leaving most of it implied instead of apparent.
• The opening fight sequence is trimmed, cutting, among other things, a second Dee-Dee kick and a taser attack which explains Batman's subsequent vision malfunction. There is a 360-degree fight sequence which is also removed, where Batman fends off the Jokerz one by one.
• White flashes have been added to the action sequences where previously there were none. Additionally, repeated punches have been mostly trimmed down to one punch.
• After the opening credits, Bruce Wayne throws a batarang that beheads a wax statue of Two-Face in the Batcave. This scene is cut and only shows the batarang return to Bruce.
• After Bonk yells at the Joker that his time is over and that he is a fake, the Joker replies "Ah, brave new world. That has such putzes in it." "Putzes" was changed to "Yutzes" in the edited version since "putz" is a Jewish word that also means "dick" as well as "fool".
• Bonk is not shot with Joker's flag-spear gun, but instead given a dose of Joker laughing gas, taking his implied death off-screen and adding a number of visual and audio edits to account for the fact. Because of this, the following loyalty oath sequence is cut.
• Blood was removed in the edited version.
• The scene where Joker cuts Batman with a knife and then stabs him in the leg was in the uncut version, which explains how Bruce got his limp and why he needed his cane for support, although he walks normally, without the limp prior to retiring as Batman in the episode "Rebirth". In the edited version, Joker instead punches Batman, though the knife can still be seen in the Joker's hand and the hole it made in Batman's costume is still visible.
• After the Joker attacked Bruce in the Batcave, when Terry returns to the cave, he found "Ha! Ha! Ha!" painted on the ground. In the uncut version, it had a blood red color. In the edited version, it had a dark purple color.
• In the uncut version, there is a scene where Batman throws a knife he used to cut himself free from the red strings at the Joker. In the edited version, the knife was removed, but the sound of the knife cutting through the strings can still be heard and the hole it made in the curtain can still be seen.
• The Joker's death scene was heavily edited. In the original, Tim fired the Joker's 'BANG!' flag/spear gun at the Joker and the projectile pierced his heart, killing him almost instantly. In the edited version, the gun was full of Joker gas and Tim does not use it. Instead he pushes the Joker into a room with hanging electrical wires and two tanks of water. The Joker crashes into one, and the wires slip down. The Joker then runs forward to get him, but instead slips and turns on the wires, electrocuting himself. Not only that, but the setup lines were changed. In the original uncut version, Joker tells Tim to "make daddy proud, deliver the punch line". After the edit and the changing of the gun from a spear gun to a Joker gas gun, the line became "make him one of us".
• During the scene where Batman and Batgirl go searching for Robin, the uncut version shows Batgirl questioning two women as to Robin's whereabouts. In the edited version it was a man and a woman. This scene may have been edited because the women were implied to be prostitutes.
• When the Jokerz visit Pryce on the Wayne Enterprises Yacht, a suggestive scene in which one of the Dee Dee sisters lays on a bed was cut from the Unrated version.
• Seatbelts were added around characters when in vehicles. There were no seatbelts in the original version.
• When Terry visits Ace (Bruce's dog) after the Joker's attack on Wayne Manor, Ace is watching a Bugs Bunny cartoon called Hare Ribbin'. A character in the cartoon repeatedly shouts "I wish I were dead!" This audio was cut from the censored version.
• In the "Our Family Memories" segment of the film, the uncut version depicts the Joker pulling out electrical cables to torture Robin. This brief sequence is cut from the censored version.
• In the Uncut version Joker's line "I'll begin with how I peeled back the layers of the boy's mind." is changed to "I'll begin with how I affected young Robin's makeover." in the edited version.
• As Joker is about to destroy Wayne Manor with the satellite beam, he asks Terry "any last words for the old Batfart?" "Batfart" was changed to "Batcoot" in the non-rated version.
• During the scene where the elderly Harley Quinn bails the Dee-Dees out of jail, her clothes are different colors. In the original version, her clothes are blue and purple. In the edited version, her clothes are red and black like her original jester outfit. Many consider this change unnecessary.

Released on October 17, 2000, the soundtrack to Batman Beyond: Return of the Joker contains music composed by Kristopher Carter as well as two tracks of music featured in the direct-to-video film.

1. "Batman Beyond: Return of the Joker (Main Title)"
2. "Industrial Heist"
3. "Meet the Joker"
4. "Joker Crashes Bruce's Party"
5. "Terry Relieved of Duty"
6. "Nightclub Fight / Terry Rescues Bruce"
7. "A Trap for Tim"
8. "Joker Family Portrait"
9. "Arkham Mayhem"
10. "Batman Defeats the Jokerz"
11. "Joker Meets His End (Again)"
12. "Healing Old Wounds"
13. "Crash (The Humble Brothers Remix)" by Mephisto Odyssey (feat. Static-X)
14. "Batman Beyond: Return of the Joker (End Title)" by Kenny Wayne Shepherd

Return of the Joker has received mostly positive reviews from critics. It currently holds an 86% rating on Rotten Tomatoes and a 7.7/10 on IMDB, the sixth highest for any Batman movie.

Nisha Gopalan of Entertainment Weekly praised the uncut version of the film, in particular how it "sheds light on the dark, obsessive relationship between the villain and his vigilante counterpart." Gerry Shamray of Sun Newspapers said that Return of the Joker "would have made a great live-action Batman movie." Ryan Cracknell of Apollo Guide called the film "an animated masterpiece."

Peter Canavese of Groucho Reviews called it an "energetic and unsettling Batman adventure," adding that it "provides a memorable showcase for Hamill's celebrated take on the Joker, and allows both McGinnis and Wayne to see action and face emotional challenges." Michael Stailey of DVD Verdict gave the uncut version a score of 92 out of 100, calling it "a taut, high-impact film" and "a must-buy to Bat-fans and animation lovers alike."

Garth Franklin of Dark Horizons had a mixed response when reviewing the uncut version, saying that "the script is pretty solid, the animation superb, and the voice performances all work well," but added that "the Terry character's personal scenes aren't anywhere near as engaging [as the scenes featuring the Joker or Bruce Wayne], and the investigative subplot doesn't work as well as it should."

While the comic based on the movie was largely uncensored, the page depicting the Joker's death had to be redone to match the movie. The rest of the comic, however, was not altered. As a result, the rest of the story refers to the Joker being shot as opposed to electrocuted and killed.

• ROTJ Page Comparison

The comic includes several scenes that did not make it to either versions of the film, such as:

• Bruce's visit to the remains of Arkham Asylum to find clues on the Joker's return. He is unknowingly followed by Terry. The Joker body is hanging from the ceiling written on his body saying "I Know". Storyboard drawings, however, do appear as deleted scenes, which were present on both versions of the DVD as part of the special features.
• Batman's interrogation of the Penguin in the flashback. Both were part of the script that got cut out of the movie due to time and pacing concerns, as confirmed in the commentary.