Atlantis was one of the great Wizard cities in ancient times. Thousands of years ago, it was destroyed by untrained magic, causing the ruins to sink to the bottom of the sea. This event led to the creation of Magic School, as the Elders wanted to prevent such a tragedy ever happening again.
In ancient times, Atlantis was the most advanced cities in the world. It was founded by Neptune, a son of Magnus, the high king of the wizard race. He was later succeeded by his daughter, Cressida. In order to share their knowledge, the wizards invited witches to come to the city. Ambrose warned the wizards it was a bad idea, as he felt witches could never be their equal, but the royal family disagreed.
The witches were educated in an academy, until they accidentally tapped into a dark power they could not control. As the dark magic destroyed the island, the prince of Atlantis, Emyr, used his magic protect his people by turning them to stone. He then used his magic to shield the tower and turned to stone as well, hoping the other cities would rescue them.
The Source of All Evil, who already felt threatened by the wizards, used this tragedy to begin his war against them, leading to the near extinction of the wizard race.
In order to obtain Auger Shells, the wizard Ambrose used the Staff of Magnus to locate the ruins of Atlantis and bring the entire island to the surface. He and his children entered the city to find the shells, though they were followed by the Chosen.
After the Chosen managed to beat the wizards, they left the island. After learning what had happened, Leo Wyatt asked the Elders to cast a protective spell around the island, so it would not be discovered by mortals. Arthur then began finding a way to free the petrified wizards.