* BadExportForYou: The European DVD has a tiny aspect ratio of 1.33:1, which is much smaller than the original 2.35:1. Luckily the original ratio was restored on both digital versions and the Blu-Ray.
* CreatorKiller: The film's failure at the box office was one of the events that led to Michael Eisner being exiled from Disney and stalled the careers of directors Kirk Wise and Gary Trousdale (who'd previously directed ''WesternAnimation/BeautyAndTheBeast'' and ''WesternAnimation/{{The Hunchback of Notre Dame|Disney}}''); Trousdale has since gone on to work on Creator/DreamWorksAnimation shorts while Wise eventually moved to a few documentaries, with his only animated feature-length film ever since being ''Bobbleheads: The Movie''. In addition, this was the first in the set of dominoes that made Disney give up on traditional animation (apart from [=DisneyToon=] Studios), which, aside from ''WesternAnimation/ThePrincessAndTheFrog'' and ''WesternAnimation/WinnieThePooh2011'', they have not revisited.
* CreatorsFavorite: Creator/CreeSummer lists Princess Kida as her favorite role, because she got to be a Franchise/DisneyPrincess.
* DeletedScene: The prologue was going to show a group of Vikings using the Shepherd's Journal and encountering the Leviathan instead of the Great Flood. This was later reused in the video game ''Atlantis: The Lost Empire -- Search for the Journal''.
* DevelopmentGag: The commentary tells a story about how there used to be a mystic named Zoltan (who used to speak in the {{third person|Person}}, for some reason) along for the ride. At one point everybody sounds off after falling down a hole. For the longest time he was still there shouting "Zoltan is okay!" even after his character had been written out of the script. Interestingly enough, Cookie's [[http://caps.pictures/200/1-atlantis-1080p/full/atlantis-disneyscreencaps.com-4437.jpg robotic mule]] can still be seen in the final film, while Rourke is accused of plotting to sell the Heart of Atlantis to Kaiser Wilhelm, which was a discarded plotline.
* DuelingMovies: This was the second Franchise/DisneyAnimatedCanon film in a row to deal with Creator/DreamWorksAnimation's ''WesternAnimation/TheRoadToElDorado'', this time with the hidden city/MsFanservice lead angle. This duel was much closer than the one with ''WesternAnimation/TheEmperorsNewGroove'' thanks to both ''Atlantis'' and ''El Dorado'' scoring about the same Rotten Tomatoes score (upper 40's), underperforming, and becoming [[StillbornFranchise Stillborn Franchises]]. ''Atlantis'' does have an edge as it got a DirectToVideo sequel, while ''El Dorado'' did worse and buried that franchise stone dead before [=DreamWorks=] could do anything with it. But given the reception of ''Atlantis''' second film from both audiences and critics, it's not much of a victory. All three films got VindicatedByHistory, though.
** Another film that duelled with this one was ''Anime/FinalFantasyTheSpiritsWithin'', with both films being DarkerAndEdgier sci-fi action/adventure animated films aimed more at a teenage audience. ''Atlantis'' performed slightly better at the box office than ''The Spirits Within'', but not by much. With reception, however, ''The Spirits Within'' was the one that performed slightly better than ''Atlantis''. It's not much of a victory on either side, but both films eventually got VindicatedByHistory.
* ExecutiveMeddling: The film was originally intended to be a creature feature adventure film. Then the Disney execs decided that they needed to get to Atlantis quicker, and so much potential was wasted.
* FakeAmerican: Canadian actor Creator/MichaelJFox once again fakes an American accent as Milo.
* InMemoriam: The movie is dedicated to Jim Varney, the voice of Cookie, who died from lung cancer partway through production.
* MultipleLanguagesSameVoiceActor: Italian voice actor Pasquale Anselmo did the voice of Vinny for the Spanish versions (both Spain and Mexico) of the film aside from the Italian version.
* TheOtherDarrin:
** Cookie's "I ain't so good at speechifyin'" line in the goodbye scene is the only Cookie dialogue delivered by Creator/StevenBarr instead of Jim Varney.
** Creator/JamesArnoldTaylor replaced Creator/MichaelJFox for the role of Milo in the sequel.
** The cutscenes in the game adaptation are actual clips of the film but with the voice actors re-dubbed by the game's VA cast.
* TheOtherMarty:
** Creator/LloydBridges was cast as Whitmore, but died just as production began. Creator/JohnMahoney was given the role instead.
** In the Spanish version, the voice of Vanessa Garcel from the Mexican dub was used for Audrey's dialogue to give her a distinctive Latina personality and accent. However, Spanish voice actress Cristina Yuste did some small takes to replace Mexican jargon words that Spanish viewers might not get, and there's rumor that she was originally slated to dub the whole character before they decided to use Garcel's recordings. Yuste also went to voice Audrey in the videogame of the film.
* PlayingAgainstType: James Garner playing a mercenary villain. Also one of the few times Creator/CreeSummer has not been a SassyBlackWoman.
* RecycledTheSeries: A cartoon series called ''Team Atlantis'' was planned, but never came to fruition; the DirectToVideo "sequel" is really just a few episodes of it strung together. Amongst the ideas proposed for this series was a crossover with ''WesternAnimation/{{Gargoyles}}'', which is {{broad|Strokes}}ly considered a canonical part of ''Gargoyles'' according to WordOfGod.
* ReferencedBy: In ''WesternAnimation/ElenaOfAvalor'' episode "The Magic Within", Elena's power-up is based on Kida with the Heart of Atlantis as well as the ''Anime/SailorMoon'' TransformationSequence.
* RefittedForSequel:
** The lava whales from ''[[WesternAnimation/AtlantisMilosReturn Milo's Return]]''.
** The original intro of Vikings being attacked by the Leviathan was used for the opening to the video game ''Atlantis: The Lost Empire -- Search for the Journal''.
* StillbornFranchise: This film's failure to perform led to the in-development sequel getting cancelled and the planned TV series getting recut into a DirectToVideo film, and also shelved the intended ''Gargoyles'' crossover.
* SwanSong: Jim Varney, who played Cookie, died from lung cancer in February 2000, over a year before its release. According to those who worked with Varney, he signed on knowing he wouldn't live to see the finished film.
* ThrowItIn:
** After Milo gets seasick the first time, he mutters "Carrots. Why is it always carrots?" This was an ad-lib from Creator/MichaelJFox and the filmmakers kept it.
** Much of Vinny's dialogue. Actor Don Novello just started rambling and the production crew liked it better than the scripted dialogue.
** Like Vinny, this applies to much of Cookie's dialogue as well.
* UrbanLegendOfZelda: In 2019, rumors that this film was going to join the list of Franchise/DisneyAnimatedCanon films slated for live-action remakes started flying around the internet, with claims that Creator/GuillermoDelToro and Creator/TomHolland were being considered to direct and star, respectively. These rumors were ultimately debunked by del Toro himself, but many people still believe them to be true, mostly because the idea of an ''Atlantis'' remake with del Toro at the helm is widely considered to be an ''awesome'' idea.
* WhatCouldHaveBeen:
** A crossover with ''WesternAnimation/{{Gargoyles}}'' was planned, but never made. Disney had been planning to make [[RecycledTheSeries a series]] out of the movie, but turned it into a direct-to-video when it underperformed at the box office. This is also true with the future of this film's merchandise: To date, the only characters from the film that still appear in the merchandise are, due to Disney's merchandising policy of marketing the villains of flopped pictures, Rourke and Helga.
*** In addition, Creator/JamesArnoldTaylor [[https://youtu.be/RJJXOJx_kSk mentioned]] here [[note]] Go to 9:50 [[/note]] that the proposed tv series would've been at least 18 episodes long.
*** Following the movie's releases, the home video cover art and even Kida's [[AdaptationalModesty face character costume]] at the parks seem to imply that Kida was originally going to predominantly be depicted in her [[spoiler: Queen dress]] as her new main outfit.
** The submarine ride at [[Ride/DisneyThemeParks Disneyland]] was originally going to be based off this film, but the film's failure resulted in that ride being based off ''WesternAnimation/FindingNemo'' instead. However, there is a restaurant at Castaway Cay called Cookie's BBQ, and part of Port Discovery's background music at Tokyo [=DisneySea=] is taken from this movie.
** Jim Hill has [[http://jimhillmedia.com/blogs/jim_hill/archive/2003/08/11/165.aspx an article]] that goes on in length about things that were cut from the movie, which includes deleted scenes of the Squid Bats and Lava Whales. There was also a plan, very early in production, for a magician character, Zoltan the Magnificent.
** A behind-the-scenes footage found on the DVD release and one of the tie-in games shows the original intro was of a group of vikings searching for Atlantis only to be attacked by a sea monster while engulfed in a storm, fully animated, voiced and with sound effects. While mystifying, the executives felt no connection nor desire to learn more about the city or its inhabitants so the intro was done over.
** At one point, Creator/MarkHamill was considered to voice Mole.
** According to the commentary on DVD and Blu-ray, during previous drafts, Mole was just a stuffy scientist, Helga and Rourke were going to have a thing for each other, Rourke was going to be a German spy, and the eye over the pyramid on the back of the US dollar was going to be used to help locate the heart of Atlantis. Also, Milo was going to be related to Blackbeard at one point.
** In an earlier version of the script, during the final battle, after failing to struck down Milo with the axe, Rourke was going to leave the axe and pull out a revolver to shoot Milo. However, Milo would have shoved the piece of crystallized glass in the revolver's barrel, leading it to backfire and rendering Rourke blind once the shards hit his eyes, causing Rourke to fall to his death. As this fate for Rourke was too similar to Helga's DisneyVillainDeath, the writers opted to rewrite the scene.
** According to WordOfGod on the DVD commentary, each tunnel would have led to a different monster, although we only see one in the finished film.
** Before Creator/JamesGarner was cast as Rourke, Creator/JackDavenport, Creator/TommyLeeJones, Creator/NathanielParker and Creator/KurtRussell were all considered.
** In a 2020 interview, Kirk Wise revealed that a true sequel called ''Atlantis: Shards of Chaos'' was being planned out at one point. It would have introduced a new villain who was described as "wearing big, scary, wool, bulky, World War I-style clothing with a frightening gas mask" and would have lead an army of mercenaries to take back Atlantis to finish Rourke's work. The twist would have been that this new villain was actually Helga Sinclair who survived her fall at the end of the first film and be brought back as a "early-20th-century cyborg."
** Helga's introduction, early on, was storyboarded differently than the final version [[https://m.youtube.com/watch?v=z0gyp1H548U as seen here]]. Her original design was also [[https://vegalleries.com/art/walt-disney/1945/atlantis-the-lost-empire-2001/atlantis-production-drawing-id-octatlantis17419 quite different]] appearing [[HotterAndSexier lusher, more sensual]] like a [[FemmeFatale film noir temptress]], more so than her [[TamerAndChaster final incarnation]]. Interestingly "prototype Helga" resembles [[Film/CoolWorld another seductive, hand drawn blonde]]. In both cases she had [[SmokingIsGlamorous a cigarette holder]]. Obviously scrubbed.
** Creator/TimCurry was originally going to voice King Kashekim instead of Creator/LeonardNimoy.
* WordOfGod: While this detail never made it into the movie, Wilhelmina Packard has BeenThereShapedHistory according to the film's makers. According to them, she worked as a research assistant and reputed mistress of Dr. Mahlon Loomis from July to November of 1875. She developed the Galvanometer, and with the help of Dr. Loomis, the concept of Hertzian Wave Application. She worked as research assistant and eventually as a full partner to Dr. Nathan Stubblefield, developing the vibrating telephone in 1888. She married Dr. Stubblefield, 1891. She secured Congressional Appropriation of $50,000 for further development of work. The appropriation was never forthcoming, for reasons known only to Congress. She divorced Dr. Stubblefield, 1893,and traveled and worked with Guglielmo Marconi, 1898-1901. She was instrumental in the December Trans-Atlanic broadcast. She worked as research fellow for Victor Talking Machine, 1902-04. She developed the Sodion Non-Regenerative Detector, 1902, and the Bornite Movable Cup Perkion Detector, 1903. She worked for Atwater-Kent 1904-1907. She helped develop Radak Type R-4 Regenerative Circuit and holds sole patent for the Orthosonic Circuit, worked for Magnavox 1907-1912, and developed AC-3-C Battery. Basically, if it was a piece of technology that was crucial shaping early telecommunications, she had a part in it.
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