According to Vector Prime's explanation, the Atlantis is one of the four Cybertronian starships that transported the Cyber Planet Keys to the four planets. The Atlantis is the ship that transported a Cyber Planet Key, the Omega Lock and transformers to Earth. Known as a city that floated on the air, it malfunctioned and fell into the Bermuda Triangle.
It was later discovered by the Autobots at the bottom of the ocean, and Vector Prime warped the Atlantis to the dark side of the moon until he and the kids could find the Omega Lock. Unfortunately, Megatron took the Omega Lock before the security system was shut down, resulting in the Atlantis' explosion.
Some time later, the kids followed Sideways, who kidnapped the Mini-Cons, to a repaired Atlantis, which Sideways had worked day and night to make into an evil hideout. They managed to escape when Starscream came back to warp the ship. Starscream would subsequently use the vessel on several occasions, notably to extract a second portion of Primus' Spark to increase his size and power once again.
In the time-space tunnel, Bud, Jolt and Reverb sabotage the engines to slow Starscream down. On Gigantion, where Sideways crashed into a fissure, Quickmix buried the Atlantis (except the bridge) in quick dry cement. The Autobots dug the Atlantis out to make a space bridge and later brought with Gigantion's inhabitants back to their proper universe.
Optimus Prime (Galaxy Convoy), in the final episode of Transformers: Cybertron "Beginning", proposed a new Space Bridge project using the power of the four Cyber Planet Keys and the four great Cybertronian ships. Many Autobots and former Decepticons joined in the project. Leaving Jetfire (Dreadrock) in charge of Cybertron, Optimus Prime led the Atlantis with the Earth Cyber Planet Key, joined by Red Alert, Safeguard, Scattorshot, Leobreaker, Menasor and Heavy Load.