Atlantis was one of the great Wizard cities in ancient times. Thousands of years ago, it was destroyed by 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. He argued with prince Emyr about this fact, though he was turned down.
Feeling humiliated, Ambrose planned to sabotage the witches and create an accident at the academy. His friend Bowan agreed and told his friend that he would set things in motion. Due to the sabotage, the witches 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. After a trip to the past with Violet, he learned that the wizards could be freed using Neptune's Trident, though only if it was wielded by Bryant due to his power of the earth.