| Image
| Title
| Number
| Airdate
| Planet(s)
| Race(s)
| Enemies
|
| "Search and Rescue" (Part 2 of 2)
| 501
| July 11, 2008
| Earth, M2S-445, M35-117
| Athosian, Hybrid
| Michael Kenmore
|
| John Sheppard and the rescue team are trapped under the rubble of one of Michael's facilities attempting to find Teyla. Col. Carter launches a rescue team of her own as Michael's hive ship approaches the planet.
|
| "The Seed"
| 502
| July 18, 2008
| M35-117
| N/A
| Jennifer Keller
|
| An alien organism takes over Dr. Keller and she begins sprouting tendrils that start overtaking the city. Carson Beckett is revived from stasis to help as the team searches for a way to cure Keller. Meanwhile, Carter is relieved of command on Atlantis and Richard Woolsey becomes the new leader.
|
| "Broken Ties"
| 503
| July 25, 2008
| Belkan, M35-117, Sarif Sur
| Satedan, Wraith
| Wraith Commander
|
| Ronon Dex is captured by Tyre who hands him over to the Wraith in order to continue his stasis among the Wraith. The Wraith betray Tyre and leave him for dead where he is found by Sheppard's team. Meanwhile, Ronon has been turned into a Wraith worshipper.
|
| "The Daedalus Variations"
| 504
| August 1, 2008
| M35-117
| Unknown Alien
| Unknown Aliens
|
| The Daedalus arrives in orbit over Atlantis despite being in the Milky Way. Investigating the ship, Sheppards team finds themselves jumping through realities, each one becomeing very dangerous and they must find a way home or they will be stuck there.
|
| "Ghost in the Machine"
| 505
| August 15, 2008
| Flying monkeys' planet, M35-117
| Asuran
| Koracen
|
| On a mission, Sheppards Jumper is affected by an unknown energy which they accidently bring back to Atlantis. The energy reveals itself to be Elizabeth Weir who uses a piece of Ancient technology to build herself a nanite body. She reveals that the rogue faction of the Asurans that survived the destruction of Asuras and they found a way to ascended, but it went wrong. Now they are all on their way to Atlantis.
|
| "The Shrine"
| 506
| August 22, 2008
| M35-117, M44-5YN, Talus
| Wraith
| N/A
|
| McKay is infected with a disease which causes him to lose his memories. As he slowly loses his mind, the rest of the team search for a way to cure him, the only cure appears to be an old Ancient outpost which happens to be under the control of the Wraith.
|
| "Whispers"
| 507
| September 5, 2008
| M35-117, Unnamed
| Michael's experiment
| Michael's experiments
|
| After an all-woman team from Atlantis finds a lab, Beckett is called in to help investigate as it is believed to be one of Michael's facilities. They soon find themselves in trouble when Michaels experiments are release.
|
| "The Queen"
| 508
| September 12, 2008
| M35-117
| Wraith
| Primary and Commander
|
| Proposing to a Wraith faction, that they take the Wraith gene therapy to remove their dependance on feeding on humans, Teyla has to pose as a Wraith queen to convince the Primary of the faction to accept the therapy.
|
| "Tracker"
| 509
| September 19, 2008
| M33-985, M35-117
| Wraith
| Wraith hunters
|
| Keller is kidnapped by a runner called Kiryk and Ronon and McKay go after her. Kiryk takes Keller to an injured little girl he rescued, however time is running out as the Wraith have arrived on the planet.
|
| "First Contact" (Part 1 of 2)
| 510
| September 26, 2008
| M35-117, M6H-987
| Vanir, Wraith
| Vanir
|
| Daniel Jackson comes to Atlantis to find a hidden lab used by Janus. After find the lab, Atlantis is infiltrated by strange aliens who kidnap McKay and Jackson and get them to activate an Ancient device. Meanwhile Todd meets with the Daedalus to help out with the plan to use the gene therapy on the Wraith.
|
| "The Lost Tribe" (Part 2 of 2)
| 511
| October 10, 2008
| M35-117, M6H-987
| Asgard, Traveler, Wraith
| Vanir, Todd
|
| McKay and Jackson discover a strange truth about their kidnappers. Todd commandeers the Daedalus after two of his cruisers are destroyed and Ronon and Keller are the only two not captured and must find a way to take back the ship. Meanwhile McKay and Jackson escaped and must find a way to stop the device before millions of people are killed.
|
| "Outsiders"
| 512
| October 17, 2008
| M35-117, Elson's planet
| Balaran, Elson's people, Wraith
| Jervis, Commander
|
| Beckett, now a traveling doctor in Pegasus comes to the aid of some villagers who's village was almost wiped out by the Hoffan plague. Taken in by others the Balarans have settled into the village. Suddenly the Wraith show up looking for the Balarans and unless they are turned in, the Wraith will destroy everyone.
|
| "Inquisition"
| 513
| October 24, 2008
| M35-117
| Latiran, Free Peoples of Riva, Tribes of Santhal
| Kelore
|
| Sheppard's team is invited by the Coalition of Planets to form an alliance. They are tricked however and taken prisoner and put on trial for crimes against the Pegasus galaxy and Richard Woolsey comes to their defense.
|
| "The Prodigal"
| 514
| November 7, 2008
| M35-117
| Hybrid
| Michael Kenmore
|
| Michael successfully infiltrates Atlantis with his hybrids looking for Teyla's child to perfect his hybrids. Sealed in the tower by a stun field, Michael and his hybrids attempt to activate the self destruct while the expedition members come up with a plan to take back the city.
|
| "Remnants"
| 515
| November 14, 2008
| M35-117
| Sekkari
| Acastus Kolya
|
| During an IOA evaluation Woolsey meets with a beautiful scientist, Vanessa Conrad, who appears to not be in the database. Sheppard is captured on the mainland by an old enemy and McKay finds a probe at the bottom of the ocean.
|
| "Brain Storm"
| 516
| November 21, 2008
| Earth, M35-117
| N/A
| N/A
|
| McKay returns to Earth with Keller to attend a presenation from an old rival, Malcolm Tunney. McKay is annoyed when his work appears to be his stolen work but must put this aside when Tunney's device cannot be shut down and lots of people are put in danger.
|
| "Infection"
| 517
| December 5, 2008
| M35-117
| Wraith
| Warriors
|
| A hive ship appears in orbit transmitting a distress call, a team investigates and finds all the inhabitants instasis stricken with a deadly disease. Finding Todd, they uncover that the gene therapy worked however many of the drones became cannibalistic and violent. Things get worse when it is discovered that the ship itself is diseased and breaking up.
|
| "Identity"
| 518
| December 12, 2008
| M35-117, Unnamed
| N/A
| Neeva Casol, Jannik, Bordal
|
| Keller accidently switches consciousnesses with a theif, Neeva Casol using an Ancient device. Neeva tries to escape from Atlantis but is stopped and the team must use her to find Neeva's body and save Keller.
|
| "Vegas" (Part 1 of 2)
| 519
| January 2, 2009
| Earth
| Wraith
| Wraith
|
| In an alternate reality, Sheppard is detective with the Las Vegas Police Department and investigates a series of murders. He tracks an assailant who jumps off a tall building and survives the drop. Taken by mysterious agents to Area 51 he find out the criminal is a Wraith who crashed on Earth during an attack and he is attempting to contact the rest of the Wraith.
|
| "Enemy at the Gate" (Part 2 of 2)
| 520
| January 9, 2009
| Earth, M35-117
| Wraith
| Kenny
|
| Todd contacts Atlantis telling them that his second in command took control of a new hive ship powered by a Zero Point Module he stole from the Asurans. Attempting to stop this ship, it suddenly leaves after encountering a signal from another reality with the location of Earth. As Earth ships are unable to stop the hive, Atlantis must return to take it on.
|
