Atlantis

Atlantis was an ancient civilisation, (PROSE: The Quantum Archangel) the existence of which was preserved only in legend after it sank beneath the waves. (PROSE: A History of Humankind)

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)

One possible version of Atlantis was located on the island of Thera. (PROSE: The Quantum Archangel)

Legend
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)

History
It had flourished in part due to the Crystal of Kronos, which had been given to them by the alien Dæmons. (PROSE: The Quantum Archangel)

Before Atlantis' destruction, the civilisation had advanced spaceflight and had reached worlds as far away as the planet Vortis, located in the Isop Galaxy. (PROSE: The Lost Ones)

Atlantis was destroyed when released the chronovore Kronos. (TV: The Time Monster)

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)

Atlantis was an exhibit in the Museum of Things That Don't Exist. (PROSE: The Taking of Planet 5)

One of Clara Oswald's splinters was an inhabitant of Atlantis. (COMIC: Blood and Ice)

Cousin Octavia visited Atlantis while working for Faction Paradox. (PROSE: Warring States)

Iris Wildthyme visited Atlantis, and told Oliver Lidenbrock of her experiences there. (PROSE: The Big Crunch)

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)

In Roma I, Atlantis was a sea city in the Roman Empire. (PROSE: Warlords of Utopia)

Minor references
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
The various televised Whoniverse visions of Atlantis, or at least the ones presented in The Underwater Menace, The Dæmons, The Time Monster, do not necessarily mesh particularly well together.

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".

Atlantide