14/07/2006      No Man's Land

After the Wraith betrayed the expedition, they head to Earth with the captured McKay and Ronon. Meanwhile, Elizabeth must answer to the IOA of her actions during the short-lived alliance and Sheppard must stop the hives from reaching Earth, whatever the cost.

21/07/2006      Misbegotten

The team has acquired victory by using the retro-virus to turn an entire hive into humans, and take them to create a colony on a Stargate-less planet, but the Wraith-humans begin to question the story the team has fed them. All the while, Richard Woolsey arrives at Atlantis to observe Dr. Weir to see if she's fit to lead the expedition.

28/07/2006      Irresistible

While harvesting Stargates for an intergalactic bridge, the Atlantis team encounters a village that adore one man to the point of insanity. He claims to have medicines to offer the team, but when Beckett investigates, he brings the man back to Atlantis smitten by the man's charm. Soon, the entire expedition falls under his spell.

04/08/2006      Sateda

Ronon is captured offworld, and his captors hand him over to the Wraith who return him to his homeworld. There, he is haunted by his past as he is forced to once again become their prey. Witness to his capture, Sheppard's team races to Sateda to help out, but Ronon's stubborn pride won't allow it.

11/08/2006      Progeny

Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, and are thriving in vast amounts of technology without any Wraith-related problems. Soon they discover they might not even be Lantean... or organic for that matter.

18/08/2006      The Real World

Dr. Weir awakens in a sanitarium outside of Washington D.C. only to find that Atlantis was a fantasy. But after a series of nightmarish visions, Weir doesn't take long to realize things aren't what they appear to be, and she is determined to return to her beloved city.

25/08/2006      Common Ground

Col. Sheppard is captured by old nemesis, Kolya, who plans to trade Sheppard for Ladon Radim, leader of the Genii. To help persuade Dr. Weir, he uses his captured Wraith to feed off Sheppard over and over again. To escape, Sheppard must find some common ground with the only one who wants to achieve the same goal.

08/09/2006      McKay and Mrs. Miller

Somewhere on earth, a young housewife has written a ground-breaking proof that could greatly benefit Atlantis. This woman is Rodney McKay's sister who has given up a career as a scientist to raise a family, and when he persuades her to come to Atlantis, another Rodney comes from an alternate reality. And he brings bad news.

15/09/2006      Phantoms

Looking for a lost Atlantis team, Sheppard and friends stumble upon a Wraith hallucinatory device, and after a few hours of research, McKay has deemed the device to be too dangerous to everyone. While attempting to leave, the DHD explodes, leaving the team stranded to become victim to the device.

22/09/2006      The Return (Part 1)

During the first test of the McKay-Carter intergalactic bridge, the Atlantis team discovers an Ancient Warship on the edge of the galaxy and they return them to Atlantis, only to find that they want the expedition gone in 48 hours. Later they must find a way to return when the Asurans invade the city.

20/11/2006      The Return (Part 2)

Major General Jack O'Neill and Richard Woolsey are captured by the Asurans during the raid on the city, so Sheppard, Weir, Beckett, and McKay disobey orders and return to the Pegasus Galaxy reuniting with Teyla and Ronon to retake the city of Atlantis, without destroying it in the process.

27/11/2006      Echoes

Starting with Teyla, everyone starts to see ghosts of Atlanteans, caused by echoes being emitted by countless whale-like creatures converging on the city. When serious side effects begin to occur, McKay discovers that the Ancients tried to teach the whales their language, and now they might be trying to warn the expedition.

04/12/2007       Irresponsible

Lucius Lavin is up to his old tricks again. He is using an Ancient Personal Shield Emitter to pose as a hero, but needs the team's help when Acastus Kolya shows up to deal with Lavin personally, until he discovers Sheppard is on the planet.

11/12/2007       Tao of Rodney

McKay acquires powerful new mental abilities through a device in the city. Nothing appears to be wrong, and after discovering several new abilities, he takes it as a blessing. But when his brain evolves too rapidly, he must choose between death and ascension.

18/12/2007       The Game

Maj. Lorne's team discovers a planet that fits the description of Sheppard and McKay's competitive video game. It turns out that it has been controlling real people through a series of Ancient satellites, who now stand on the brink of war and destruction.

08/01/2007       The Ark

Colonel Sheppard's team discovers a space station where the last of a race of humans remain. They soon discover, however, the entire population is in danger when the station is damaged through the suicide of a recently awoken resident.

15/01/2007       Sunday

In the twenty-four hours of the expedition's "required" day off, an unexpected explosion kills three and injures more. After further analysis, McKay discovers a device has given two people explosive tumors, and one has already gone off. Beckett tries to remove the other, but will result in the loss of an important face in Atlantis.

22/01/2007       Submersion

The team discovers a Lantean drill platform at the bottom of the ocean floor which may be an alternative to ZPMs, but during their visit, they are ambushed by an old and angry enemy, a wraith queen. When they capture her, she reveals that her cruiser is on self-destruct, threatening to take Atlantis and the drill with it.

29/01/2007       Vengeance

Now that every Wraith sees Michael an "unclean thing," he has been experimenting with Iratus bugs, creating monsters to protect himself and create an army to rule the galaxy. When the team stumbles on one of his labs, they are attacked by countless creatures.

05/02/2007       First Strike

When the Apollo arrives from Earth, they launch a preemptive strike against the Asurans when it is discovered that the Replicators are building a fleet of ships. When the armada is destroyed, a weapons satellite appears above the city, and unless they can fly the city away from Lantea, Atlantis will be no more.