The original cut of this film was much more violent than the final version, including, among other scenes, the young Robin/Tim Drake shooting and killing a character with a spear gun. After the tragedy in Columbine, studio pressure forced a new cut of the film be produced. Several scenes were snipped and re-edited to achieve the final PG rating. After the film had been released for some time, the original PG-13 version was released separately as an uncut version.
The orbital weapons platform that creates a beam of light before it destroys is taken from the 1988 Japanese animated film Akira (1988) as is the basic design for the orbital weapons platform itself. In fact, one of the directors of animation at Tokyo Movie Shinsa (the Japanese animation company where most of the film was done) was the actual animator of the scene in Akira (1988) when Kaneda was briefly chased by the beam from the orbital system. When the scene of Terry being chased by the beam came up, the director snagged the storyboarding duties on it for himself, under the auspices of aiming to top himself.
When Bruce is checking the future-Joker's voice against that of the past-Joker, the clip is a newly animated (but previously scripted) segment from "Holiday Knights," which was the first episode of the redesigned Batman cartoon that appeared on the WB network.
The voice of Ghoul was provided by Michael Rosenbaum, who did several voices for the television series "Batman Beyond." While in the recording studio, he would often do a Christopher Walken impression that the producers found hilarious. When they were commissioned to create this film, they wrote the part of Ghoul for Rosenbaum's Walken impression. He would later reprise the role in an episode of Justice League (2001), a series on which he also voiced series regular The Flash. Later Rosenbaum would play the role of Supermans enemy Lex Luthor in the TV series Smallville.
When Terry lists possible explanations for the Joker's return, he mentions being "placed in suspended animation due to floating around in a block of ice." This is a reference to the Marvel Comics character Captain America, who was found floating in ice by the Avengers in the '60s.
Although the final version is rated PG with the director's cut being PG-13, it's a possibility that this is the only film for Cartoon Network's Cartoon Theatre to air a PG-13 film, and the first Cartoon Network's airing of a PG-13 film.
The Joker's "brave new world" quote in his first scene is a reference to a line from Shakespeare's "The Tempest", Act V, Scene 1, 2: "O wonder! How many goodly creatures are there here! How beauteous mankind is! O brave new world, That has such people in't."
The 'Original Uncut Version' of the film, that was rated PG-13, would be the default version for every video release 2 years after the initial home video release. The censored version would no longer be available to the public on future DVD and Blu-Ray releases. Some DVD's still have the censored version as the default (which some consider more disturbing due to the fact that the violence is off-screen and includes disturbing screams from some of the characters).
A second direct-to-video movie based on Batman Beyond (1999) was planned if this movie sold well; it did not, and the second movie was canceled. However, most of the major plot points of the proposed second movie were used five years later to develop Justice League Unlimited: Epilogue (2005).
The trivia items below may give away important plot points.
Tim Drake's transformation into The Joker at the end of the film is almost identical to Kirk Langstrom's transformation into Man-Bat during the climax of the first "Batman: The Animated Series" episode "On Leather Wings".
Although the Joker is generally thought to have been destroyed for good in this movie, he is not actually completely gone, as he has a still-living counterpart in an alternate universe introduced in the "Justice League" episode, Justice League: A Better World: Part II (2003), in which the Joker has been lobotomized by that dimension's Superman and now serves as the superintendent of Arkham Asylum. However, this alternate Joker's status, by the time of the movie, is unknown.
At the end of the film, it is revealed that Harley Quinn is the grandmother of the Dee sisters. If that's the case, either Harley had children, or considers Tim Drake to have been her son, and the Dees are Tim Drake's daughters, making Harley Quinn their adopted grandmother.
Barbara Gordon tells Terry that Harley Quinn's body is never found. That's strange, considering in the series, Harley Quinn's costume is seen on display in the Batcave. Either this was an oversight in storytelling, or Batman found another of her costumes and kept it after her "Death".