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Atlantis refers to several concepts in the Transformers franchise.
Atlantis appears in Transformers: Victory, where it is raised from the depths of the ocean by Deszaras in order to secure its energy to reenergize his space fortress. This abrupt shift causes massive tidal waves that the Autobots are forced to respond to, leaving them unable to stop the Decepticons from loading the Thunder Arrow up with Energon. Having acquired all that he needs, Deszaras leaves the continent to sink back into the ocean, abandoning the Dinoforce at the same time.
The Atlantis is one of four ancient Cybertronian vessels that took the Cyber Planet Keys away from Cybertron long ago in Transformers: Cybertron; it landed on Earth, inspiring the legend of the lost continent.
Though not mentioned by name in Transformers: Exiles, one of the Atlantis' sister ships, the Ogygia, is mentioned as having ferried Cybertronian colonists to Velocitron as in Cybertron; it is thus likely that a version of the Atlantis also existed, though it is unknown if it transported any Transformers to Earth.