Atlantis was built millions of years ago by the Ancients, who called it Atlantus. The city resided in Antarctica on Earth until five to ten million years ago, when a devastating plague prompted the Ancients to relocate it to the Pegasus galaxy. There, it served as the Ancients' capital as they built a new system of Stargates and seeded many worlds with humans.
However, the Ancients' activities gave rise to a powerful new species, the Wraith. With their vastly superior numbers, the Wraith drove the Ancients from their holdings until only Atlantis was left, defended by its powerful shield and a network of armed satellites.The Wraith laid siege to Atlantis for years; The Ancients submerged the city for protection but, unable to see a path to victory, eventually chose to return to Earth through the Stargate.
There they merged with the native human population, and their accounts of Atlantis gave rise to the classical myth of the Lost City. Atlantis itself lied on the ocean floor, empty and dormant, for ten thousand years.