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Atlantis is known on Earth as a legendary continent or city which vanished cataclysmically into the sea ages ago. But legends are funny things...
American animated series
It is suggested that the undersea city of Sub-Atlantica, populated by mer-men, was the inspiration for the legend of Atlantis.
Victory animated series
The existence of Atlantis itself would be proven in the future, during Deathsaurus's campaign against Earth. With its location identified by Hellbat, the city was raised by the Decepticons, and its vast supply of energy pillaged to re-energize Deathsaurus's space fortress. The massive tidal waves created by the rising of Atlantis kept the Autobots occupied protecting coastal cities that were devastated, and the Decepticons escaped with the energy. The Dinoforce, however, were abandoned on Atlantis by Deathsaurus, and were swept away as the city fell back beneath the waves.
Armada animated series
When an ancient Earth civilisation seized control of the power of the Mini-Con Star Saber, the forces they unleashed in war with another nation wound up sinking their city into the ocean. The stasis panel of one of the Saber's components remained in the ruins, where it activated in 2010, alerting the Autobots on Earth to its presence. Autobot ally Carlos Lopez was smitten by a self-aware hologram of one of the city's former inhabitants, but was forced to accept that she was not truly real as a battle with the Decepticons destroyed what was left of the ruins.
Although Rad White compared the ruined city to Atlantis, further discoveries several decades later would make it clear that it was not the actual place.
The Earth legend of Atlantis was revealed to have been inspired by an ancient Cybertronian starship that went by that name - one of four dispatched from the planet eons in the past, with the intention of creating a universe-wide space bridge network. The Atlantis headed for Earth, containing a Cyber Planet Key and the Omega Lock. It hovered in the sky above the planet for a time, until a malfunction caused it to crash into the ocean, laying down the basis for the stories that would be passed down through the ages by human kind.
The symbol of the Omega Lock was emblazoned upon the Atlantis, and that symbol went hand in hand with the legend, becoming a piece of popular culture to the extent that, by 2030, it was being featured on album covers and T-shirts. When Optimus Prime's Autobots returned to Earth in that year, the ancient Transformer Vector Prime recognised the symbol, setting both Autobot and Decepticons off in a search for the Omega Lock itself. An Autobot civilian in the guise of a submarine eventually discovered the Atlantis buried at the bottom of the Atlantic Ocean; when the Autobots entered the craft, its warp engines activated and teleported the ship to the dark side of the moon. With the aid of the Recon Mini-Con Team and the Autobots' three human allies, Vector Prime was able to locate and secure the Omega Lock before the Decepticons.
The Atlantis was left floating by the moon until Sideways teleported the injured Starscream there to recuperate. When Sideways later kidnapped the Mini-Cons, the kids followed him through his warp gate and emerged on the Atlantis. Although Coby, Lori and Six-Speed were later able to escape, Bud, Jolt and Reverb were left stranded on the Atlantis as the ship warped away. The ship later passed through the spatial rift leading to Gigantion, the Giant Planet, after which Bud and the Mini-Cons were able to escape and reunite with the Autobots.
When Starscream was defeated in battle with Galvatron, the Atlantis fell back into Autobot hands, and was used to return to Cybertron, where it was merged with the other three ancient starships to create the Ark, through which Primus channeled his power and sealed the black hole.
With the threat of the black hole and Galvatron dispatched, a new space bridge program was introduced, and the four starships again departed for the far reaches of the galaxy.
Known members of the crew of the Atlantis on this voyage include