- You may be looking for the space shuttle Atlantis.
By the 21st century, humanity believed Atlantis to be purely fictional. The Twelfth Doctor rebuked this. (PROSE: A History of Humankind) During the Doctor's many lives, they had encountered at least three possible versions of Atlantis. (TV: The Magician's Apprentice) The Twelfth Doctor himself noted that it may have existed several times. (PROSE: A History of Humankind)
The earliest known version of Atlantis was founded on the volcanic island Thera. These Atlanteans worshipped many of the same gods as the ancient Greeks. The island's Temple of Poseidon was erected around 2000 BC; Dalios, who witnessed its construction as a young man, was king of Atlantis 537 years later. (TV: The Time Monster) The civilisation flourished partly because of the Crystal of Kronos, which had been given to the Atlanteans by the alien Dæmons. (PROSE: The Quantum Archangel)
An underwater Atlantean outpost survived beneath the ocean, south of the Azores. Around the 20th century, Professor Zaroff discovered the survivors and proposed to raise their settlement from the ocean floor. This would have destroyed the Earth. Zaroff died in the attempt due to the Second Doctor's intervention. (TV: The Underwater Menace)
Later, the Dæmon Azal pointed to the destruction of Atlantis as a warning as to what might happen if he considered Earth, a planet that the Dæmons had helped along, a failed experiment. (TV: The Dæmons)
Later in history, it was believed that Atlantis had been situated in middle of the Atlantic Ocean. However, by the 1970s or 1980s, this idea was considered outdated; the new consensus was that Atlantis had been part of the Minoan civilisation, and located on Thera. (TV: The Time Monster)
A textbook from Coal Hill School Library stated that Atlantis was a fictional island first mentioned by Plato - a Greek philosopher. It was supposedly located "beyond the Pillars of Hercules". The island went to war with Athens, fell out of favour with the gods and sank beneath the waves. (PROSE: A History of Humankind)
Other locations of the same name
The Epoch created a world that was very similar to Atlantis. It was destroyed by Bernice Summerfield and Ruth. (AUDIO: The Kraken's Lament, The Temple of Questions, Private Enemy No. 1, Judgement Day)
The Sixth Doctor once told his companion Flip that there were several versions of Atlantis. (AUDIO: Antidote to Oblivion) The conflicting locations of Atlantis were later used to confuse the directional computer of the Scavenger. (AUDIO: Scavenger) In the Doctor's next incarnation, he mentioned that there were three "Atlantises" and that he had visited all of them. (PROSE: Transit) Among the various visits made by the Doctor across the globe in the past, three possible versions of Atlantis were noted by Jac as UNIT in the 2010s compiled a list of his appearances in order to deduce where the Twelfth Doctor had gone for his final destination. (TV: The Magician's Apprentice)
The Fourth Doctor compared the "lost" human space station Nerva Beacon to Atlantis; they were both the subject of legend. (TV: The Sontaran Experiment) He later recalled the Atlanteans as one of the civilisations which had created twisting underground passageways which he had to run up and down. (PROSE: A Device of Death)
In 1939, the Seventh Doctor asked Heinrich Himmler if he believed in Atlantis, which according to the Nazis was "the secret home of the Master Race." Himmler affirmed that he did. (PROSE: Timewyrm: Exodus)
The Time Agency and the Hokrala Corp were both involved in the sinking of Atlantis. This event was considered a failure for the Time Agency. Jack Harkness was also involved. (PROSE: The Undertaker's Gift)
Behind the scenes
Noting this, former Producer Barry Letts' noted in his introduction to the first edition of The Doctor Who Programme Guide that Atlantis had three different and incompatible explanations for its destruction. The line in Transit references this. This point would later be enforced in two Big Finish audio plays, and an off-hand reference made on television in The Magician's Apprentice to "three possible versions of Atlantis".