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There was a time when many theatrically-released animated Disney movies scored one or more direct-to-video sequels. Atlantis: The Lost Empire was part of this group, but it turns out that there were originally plans for the 2001 movie to get a follow-up that also would have been shown on the big screen.
This information comes from Kirk Wise, who co-directed Atlantis: The Lost Empire with Gary Trousdale. When asked if he’d mapped out any Atlantis sequels in a recent interview, Wise responded:
Believe it or not we did. [Story supervisor] John Sanford, Gary and I actually concocted an idea for a sequel to Atlantis. It had no relation to the Atlantis TV series that was being developed at Disney Television Animation. This was a feature-length, full-on, full-blown sequel to Atlantis.
It’s important to note that the direct-to-video Disney sequels hailed from Disneytoon Studios as opposed to Walt Disney Feature Animation, which has since changed to Walt Disney Animation Studios. So for Atlantis: The Lost Empire to have been in consideration for a theatrical sequel was a big deal, as until that point, the only big screen follow-ups the folks at the Mouse House’s animated film division has churned out were The Rescuers Down Under and Fantasia 2000, with Ralph Breaks the Internet and Frozen II joining that lineup in 2018 and 2019, respectively.
As for what this Atlantis: The Lost Empire theatrical sequel would have been about, while Kirk Wise couldn’t recall its title while speaking with Collider, he did note that it would have involved a masked villain who was eventually revealed to be a familiar face. As Wise put it:
We were going to have a new villain in the story. The villain was going to be wearing big, scary, wool, bulky, World War I-style clothing with a frightening gasmask to obscure it’s face; a little Darth Vader-esque. And this villain was going to try and retake Atlantis and finish the job that Rourke was unable to accomplish. And the big twist in the climax of the movie is that the villain is unmasked and it turns out to be Helga Sinclair. Plot twist!
For those who need a refresher on Atlantis: The Lost Empire, Helga Sinclair, voiced by Claudia Christian, was the second-in-command to James Garner’s Commander Rourke on the expedition to Atlantis, meaning that she was in on the plot to steal the city’s protective crystal. Unfortunately for her, she was betrayed by Rourke, who tossed her from the Gyro-Evac during his escape. Barely clinging to life, Helga managed to fire off a flare gun to destroy the balloon, thus preventing Rourke from fleeing.
Given the extent of her injuries and the fact that the area where she fell soon after became engulfed by lava, it’s assumed that Helga Sinclair died. However, had this particular Atlantis: The Lost Empire sequel moved forward, then she would have somehow survived to become what Kirk Wise described as a “an early-20th-century cyborg” who formed “her own team of mercenaries.”
Alas, not only was Atlantis: The Lost Empire met with mixed critical reception, it didn’t make much of a splash at the box office, which is presumably what killed the chances of this sequel happening. And while there also a TV series in development called Team Atlantis, that was scrapped too, resulting in the three episodes that had been completed being stitched together to make Atlantis: Milo’s Return.