第 3 季 共 20 集
播出时间：2006年7月14日
第 1 集 No Man's Land (2)
播出时间：2006年7月14日
The team desperately attempts to stop two Wraith hive ships from reaching Earth. Sheppard must rely on an old foe to rescue McKay and Ronon.
第 2 集 Misbegotten (3)
播出时间：2006年7月21日
The Atlantis team must decide the fate of a colony of Wraith they have turned into humans. Dr. Weir must defend her leadership when she is evaluated by the I.O.A.
第 3 集 Irresistible
播出时间：2006年7月28日
Sheppard's team meets an obnoxious man who is adored by all thanks to a secret that he carries -- and who has an unexpected affect on them.
第 4 集 Sateda
播出时间：2006年8月4日
Ronon Dex is captured by the Wraith and returned to his homeworld, where he is haunted by his past as he is forced to once again become their prey.
第 5 集 Progeny
播出时间：2006年8月11日
Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, but discover that they may not have left Atlantis in peace.
第 6 集 The Real World
播出时间：2006年8月18日
Elizabeth Weir wakes up in a mental institution, where she is told that the expedition to Atlantis and the Stargate are figments of her imagination.
第 7 集 Common Ground
播出时间：2006年8月25日
Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.
第 8 集 McKay and Mrs. Miller
播出时间：2006年9月8日
Rodney McKay is reunited with his estranged sister back on Earth, who has given up a brilliant career as a scientist to raise a family.
第 9 集 Phantoms
播出时间：2006年9月15日
Sheppard and Ronon are influenced by a mind-altering device created by the Wraith while on a mission to rescue a lost team.
第 10 集 The Return (1)
播出时间：2006年9月22日
The Atlantis expedition is stunned to learn that a ship full of Ancients is returning to reclaim their lost city.
第 11 集 The Return (2)
播出时间：2006年11月20日
The Atlantis team goes against orders to try and save Atlantis from Replicator control -- and to rescue General O'Neill and Richard Woolsey, who are trapped in the occupied city.
第 12 集 Echoes
播出时间：2006年11月27日
The inhabitants of Atlantis begin to suffer ill effects when the planet's whale population begins migrating to the island city, bringing an unexpected harbinger of doom.
第 13 集 Irresponsible
播出时间：2006年12月4日
The team finds Lucius Lavin manipulating the people of another hapless planet, using Ancient technology to pose as an invincible hero.
第 14 集 Tao of Rodney
播出时间：2006年12月11日
After an Ancient device gives Rodney superhuman powers, his enhanced brilliance is checked only by his impending death -- unless he can learn how to ascend.
第 15 集 The Game
播出时间：2006年12月18日
Sheppard and McKay discover that their competitive video game has been controlling a planet of real people, who now stand on the brink of war.
第 16 集 The Ark
播出时间：2007年1月8日
The team discovers the last of a civilization in suspended animation, whose survival is at risk when their station is critically damaged.
第 17 集 Sunday
播出时间：2007年1月12日
The team tries to relax during a mandatory day off, until an explosion leaves three people dead -- and reveals that one scientist is a walking time bomb.
第 18 集 Submersion
播出时间：2007年1月15日
The team discovers an Ancient drilling station deep beneath the surface of the ocean, only to find that a Wraith queen is still alive there.
第 19 集 Vengeance
播出时间：2007年1月29日
The Atlantis team investigates the disappearance of one of their allies, only to find an old enemy engineering a race of powerful monsters.
第 20 集 First Strike (1)
播出时间：2007年2月5日
An unstoppable energy weapon leaves Atlantis under seige after Earth launches a preemptive attack against a very powerful enemy's homeworld.
