The sleepy Pacific Northwest town of Eureka is hiding a mysterious secret. The government has been relocating the world’s geniuses and their families to this rustic town for years where innovation and chaos have lived hand in hand. U.S. Marshal Jack Carter (Colin Ferguson) stumbles upon this odd town after wrecking his car and becoming stranded there. When the denizens of the town unleash an unknown scientific creation, Carter jumps in to try to restore order and consequently learns of one of the country’s best kept secrets.

The story of Stargate Atlantis follows the cliffhanger episode on Stargate SG-1's seventh season finale "Lost City", where SG-1 found an outpost made by the race known as the Ancients in Antarctica. After the events of Stargate SG-1 season eight premiere "New Order", the Stargate Command sends an international team to investigate the outpost. Soon, Dr. Daniel Jackson discovers the location of the greatest city created by the Ancients, Atlantis. The story unfolds when the members of the expedition encounter the Wraith, the race that defeated the Ancients ten thousand years ago.