Batman Beyond proved popular enough during its initial run than a spin-off film was green-lit; this film, Return Of The Joker, featured Terry McGinnis facing off against the inexplicably returned nemesis of his mentor and predecessor.
However, the film's production occurred in the wake of the 1999 Columbine High School shooting, a tragedy that had sparked growing concern about the effects of violence in media consumed by adolescents. The film's initially released cut was thus censored, with the original cut being released as the "Uncut Version" in 2002. Let's take a look at the differences between the two versions.
10 Safety First
After the scene of the Joker making his public return at a Wayne Enterprises event, a short scene follows of Terry chauffeuring Bruce back to Wayne Manor; Bruce sits silently while Terry speculates wildly about how the Joker is back. The only difference between the two cuts' presentation of the scene is that, in the censored version, Terry and Bruce are both clearly wearing seat belts. An incredibly minor, cosmetic change to be sure, but one that reflects the circumstances under which the censored version of Return of the Joker was made.
9 No Two-Face Dummy Decapitation
The Beyond-era Batcave is stocked with mannequins of Bruce's old rogues gallery, and one of them gets focus in the second scene of Return of the Joker. Just before Terry returns to the Batcave, Bruce is shown throwing a Batarang through the cave, with it decapitating a Two-Face before making its way back to him. A change arguably for the best; Bruce's obvious pleasure rings a little cold-blooded, even for him, given he'd been friends with Harvey Dent prior to the Gotham DA's disfigurement.
8 Harley's Outfit Is Different Color
Harley Quinn seemingly falls to her doom during Return of the Joker's extended flashback scene, but was saved by what amounts to divine intervention. HQ creator/ROTJ screenwriter Paul Dini, hesitant to kill off the character he considered his greatest contribution to the Batman mythos, inserted a short scene near the film's end to confirm her survival.
The scene in question features an aged Harley and reveals that not only did she reform after the Joker's death, but that the Dee Dee twins are her grand-daughters. However, in the censored version, her clothes are changed from blue-and-purple to the same red-and-black as her super-villain outfit, to make it (even more) obvious who this old woman is supposed to be.
7 No Prostitutes In Flashback
Many of the changes to Return of the Joker manifest in the film's flashback that chronicles the final battle between the original Batman and Joker. An early part of the sequence features Batman and Batgirl scouring the Gotham City underworld for clues as to the abducted Robin's whereabouts. A quick shot in this montage included Batgirl grilling two scantily-clad women, obviously street-workers, who'd previously appeared as contacts of Barbara in The New Batman Adventures episode The Ultimate Thrill (incidentally, the woman on the left was used as the design basis for Black Canary in Justice League Unlimited). The censored version replaces the pair with a random man & woman.
6 Opening Fight Is Less Violent
The film's opening features Terry attempt to stop a robbery by the Jokerz gang, resulting in an extended, six-on-one fight scene. Due to the aforementioned concerns about violent content, however, the censored version's fight is shorter and features less onscreen fisticuffs, with white flashes added between the cuts to fill in the gaps in continuity.
5 Joker's Message Is In Purple, Not Red
The Joker, having learned Batman's true identity shortly before his original demise, infiltrates the Batcave and doses Bruce with his Joker Venom. Fortunately, Terry arrives just in time to administer the antidote to Bruce.
Before getting to Bruce, Terry finds a message left by the Joker across Wayne Manor; "HA!" written several times over in gigantic font. In the Uncut version, the writing is colored red, hinting it may be written in blood, while the censored version has the lettering colored purple instead, meaning its likely nothing but spray paint.
4 Batman Doesn't Throw A Knife At The Joker
When the Joker and Harley reveal their handiwork on Tim Drake, Bruce is so enraged that he throws a pocket-knife at the Joker's head with clear lethal intent. Unfortunately, the Joker ducks and the knife merely cuts through a curtain behind him instead. This chain of events is cut from the censored version, though its absence results in a continuity error; the gash in the curtain can still be seen behind the Joker despite there being no knife to make it.
3 Joker Punches Batman Instead Of Stabbing Him
After the Dark Knight corners him in the Arkham ruins, the Joker use a knife to slash Batman's chest then stab him in his upper left leg. The residual injuries from the wound to his leg are confirmed to be the reason Bruce requires a cane in his later years, as shown throughout Batman Beyond. However, in a similar case to the scene mentioned above, the Joker's knife was cut outright from the Censored version, with the Joker simply (and far less dramatically) punching Batman instead.
2 How Bonk Dies
Bonk, a member of the Jokerz, is shown throughout the film's opening scene as the headstrong muscle of the group; his impatience backfires on him when he talks back to the Joker.
In the uncut version, Bonk is definitely killed with a spear through the heart, whereas in the censored version, he's merely doused with Joker venom, leaving his ultimate fate more ambiguous.
1 How The Joker Dies
The most significant change between Return Of The Joker's two cuts is how the titular villain perishes in the flashback sequence. The flashback climaxes with the Joker tossing a spear gun to the Joker-fied Robin to finish Batman off; in the uncut version, Tim shoots the Joker with the spear gun, whereas in the censored cut, he tosses the gun away and pushes the Joker into some loose wires hanging from the ceiling, causing the clown to be electrocuted. The different scenes utilize different dramatic effects - in the original cut, the Joker's full death plays out onscreen; he gasps out a few final words ("That's not funny... that's not...) before the light leaves his eyes and his freshly vacated body falls over. This scene is conscious of the "if there's no body, they aren't dead" rule of fiction, a rule the Joker had used to cheat death many times in the DCAU; by lingering on his demise, the film differentiates from his past "deaths" by making it clear that this time, his luck had run out. The redone version instead operates on the "what's left unseen is scarier" principle; just as the Joker's electrocuted, the film cuts away to Batgirl hearing a blood-curdling scream.