| Image
| Title
| Number
| Airdate
| Planet(s)
| Race(s)
| Enemies
|
| "No Man's Land (Part 2 of 3)"
| 301
| July 14, 2006
| Earth, Lantea
| Asgard, Wraith
| Wraith Queen
|
| Two WraithHive Ships used the alliance to upgrade their hyperdrives to reach Earth. While the Daedalus and Orion are sent to dispatch them, McKay and Ronon escape from their cocoons, and Sheppard uses his F-302 to attach himself on one of the ships to ambush them.
|
| "Misbegotten (Part 3 of 3)"
| 302
| July 21, 2006
| Earth, Lantea, M8G-352
| Asgard, Human-form Wraith, Wraith
| Michael Kenmore
|
| The Atlantis Expedition stopped the Wraith from reaching Earth, and now that they turned Human, they send them to an isolated world to teach them to administer the retrovirus themselves. However, some of them, including Michael Kenmore is starting to remember their past.
|
| "Irresistible"
| 303
| July 28, 2006
| Lantea, Lucius' planet, M6H-491
| Wraith
| N/A
|
| The Atlantis Expedition encounter Lucius Lavin, a highly obnoxious man, but everyone in his village seem to love him. After visiting Atlantis, McKay and Sheppard notice that everyone in the city is starting to fall for him, and it is up to them to figure out why.
|
| "Sateda"
| 304
| August 4, 2006
| Keturah's planet, Lantea, Sateda
| Wraith
| Wraith Leader
|
| Ronon Dex is noticed by the villagers he once visited during his time as a runner. After getting turned in by the Wraith, he is implanted with another Wraith tracker and dropped off on his abandoned homeworld, Sateda, where he is forced to become a runner again.
|
| "Progeny"
| 305
| August 11, 2006
| Asuras
| Asuran
| Oberoth
|
| The Atlantis Expedition makes first contact with the Asurans, who claim that they are the last of the Ancients. However, after holding the team prisoner, they learn that they are not people, but machines; Replicators, and they plan to destroy Atlantis.
|
| "The Real World"
| 306
| August 18, 2006
| Lantea
| Asuran
| N/A
|
| Elizabeth Weir awakens in a psychiatric hospital outside Washington D.C. where she is told that she never left Earth, and the entire Stargate Program, and Atlantis never existed.
|
| "Common Ground"
| 307
| August 25, 2006
| Kolya's planet, Lantea, Unnamed
| Genii, Wraith
| Acastus Kolya
|
| John Sheppard is captured by Acastus Kolya, who wants the Expedition to hand over Ladon Radim, in exchange of returning Sheppard. Sheppard is also imprisoned with a Wraith feeding on him, and the two form an unlikely alliance to escape the base.
|
| "McKay and Mrs. Miller"
| 308
| September 8, 2006
| Earth, Lantea
| Asgard
| N/A
|
| Jeannie Miller, Rodney McKay's sister has thought up a theory to bridge two Universes together. Stargate Command, and later Rodney convinces her to come to Atlantis to reform Project Arcturus. However, soon, another McKay appears in front of everyone's eyes.
|
| "Phantoms"
| 309
| September 15, 2006
| Lantea, M1B-129
| Genii, Wraith
| N/A
|
| The First Atlantis Reconnaissance Team travel to M1B-129 to retrieve a missing team, but come across a WraithMind manipulator, making the team see things things that aren't there.
|
| "The Return (Part 1 of 2)"
| 310
| September 22, 2006
| Earth, Lantea, New Athos
| Ancient, Asuran, Genii
| Cetus, Talus
|
| While testing the McKay-Carter Intergalactic Gate Bridge, the Daedalus picks up an Ancient warship, the Tria, who retake control of Atlantis, and the Expedition is expelled to Earth. However, the Asurans are heading straight for Atlantis.
|
| "The Return (Part 2 of 2)"
| 311
| November 20, 2006
| Earth, Lantea, New Athos
| Asuran
| Cetus, Talus
|
| The First Atlantis Reconnaissance Team reunites to take out the Asurans, who have taken control of Atlantis, and plan to use Niam, who is drifting in space over Lantea. Meanwhile, O'Neill and Woolsey do their best to avoid capture.
|
| "Echoes"
| 312
| November 27, 2006
| Lantea
| Ancient, Flagisallus
| N/A
|
| Teyla Emmagan starts seeing "ghosts" of Ancients wondering Atlantis, and soon, other people starts seeing them also. The visit from a group of Flagisallus are related, when they use the "ghosts" to warn the Expedition of a Coronal mass ejection.
|
| "Irresponsible"
| 313
| December 4, 2006
| Lantea, M65-PL8
| Genii
| Acastus Kolya
|
| Atlantis 1 travels to a planet to meet a "hero", only to find Lucius Lavin, who plays off Genii mercenaries to win the hearts of the village. However, the mercenaries soon contact Acastus Kolya to capture Sheppard's team.
|
| "Tao of Rodney"
| 314
| December 11, 2006
| Lantea
| N/A
| N/A
|
| Rodney McKay gates "zapped" by a device, where his brain quickly evolves to that of the Ancients to achieve Ascension, and he gains super powers. However, he must learn to ascend, or he'd die, but it isn't easy.
|
| "The Game"
| 315
| December 18, 2006
| Lantea, M4D-058
| Geldaran, Hallonan
| N/A
|
| Evan Lorne reports back from M4D-058 and tells them they encountered a race of humans who has McKay's face on their flag. They learn that a game McKay and Sheppard were playing is actually happening in reality. However, this also causes friction between McKay and Sheppard's worlds, who are on the brink of war.
|
| "The Ark"
| 316
| January 8, 2007
| Lantea
| N/A
| Jamus
|
| 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.
|
| "Sunday"
| 317
| January 15, 2007
| Lantea
| N/A
| N/A
|
| While the Atlantis Expedition tries and relax on a regular Sunday, a mysterious explosion rocks the city, leaving three people dead. It is later revealed that a scientist is a walking time-bomb, and has to be stopped. However, the attempt to resolve the problem will result in the loss of an important figure in Atlantis.
|
| "Submersion"
| 318
| January 22, 2007
| Lantea
| Wraith
| Wraith Queen
|
| The Atlantis Expedition explore a Mobile drilling platform under the ocean of Lantea. However, due to Teyla's background, a Wraith Queen awakens after being stuck in a nearby crashed cruiser for 10,000 years.
|
| "Vengeance"
| 319
| January 29, 2007
| Lantea, Taranian settlement
| Bug People
| Michael Kenmore
|
| The Taranians have failed to contact Atlantis, so Atlantis 1 is sent to investigate. They find the settlement abandoned, and soon find them all dead, by Michael Kenmore's experimenting.
|
| "First Strike (Part 1 of 3)"
| 320
| February 5, 2007
| Asuras, Lantea
| Asuran
| Oberoth
|
| The new Earth battle-cruiser Apollo arrives in Atlantis to launch a preemptive strike against an armada of Asuran ships preparing to take off to Earth. However, after the strike is finished, a weapons satellite appears above the city and attacks its shields. If they cannot find away out of the situation, Atlantis will be no more.
|
