Search and Rescue (Part 2 of 2)" 501
July 11, 2008
Earth, M2S-445, M35-117
Lt. Colonel John Sheppard and his team are trapped under the rubble of Michael's facility in order to rescue Teyla Emmagan. As Colonel Samantha Carter launches a team to rescue the rescuers, little do they know that Michael Kenmore is also searching the planet for the survivors.
The Seed" 502
July 18, 2008
When a mysterious alien organism takes Dr. Jennifer Keller as its host, the newly revived Dr. Carson Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis. In the meantime, Richard Woolsey officially joins the team, having been chosen as Colonel Samantha Carter's replacement to lead the Atlantis expedition.
Broken Ties" 503
July 25, 2008
Belkan, M35-117, Sarif Sur
Ronon Dex is captured by Tyre, who wants to hand him to the Wraith in order to maintain his role in their circle. However, when the deal turns sour, and Tyre is left for dead, the Atlantis expedition persuade him to take back their friend. Meanwhile, The Wraith turn Ronon into a Wraith worshipper.
The Daedalus Variations" 504
August 1, 2008
The Atlantis expedition mysteriously finds the , abandoned and drifting in space. When Daedalus Lt. Colonel John Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.
Ghost in the Machine" 505
August 15, 2008
Flying monkeys' planet, M35-117
While on a mission, Lt. Colonel John Sheppard's team inadvertently brings a mysterious entity to Atlantis. They soon learn that the entity is nothing more than Dr. Elizabeth Weir, who was thought to have been killed after her capture by the Asurans.
The Shrine" 506
August 22, 2008
M35-117, M44-5YN, Talus
Dr. Rodney McKay is infected with the Pegasus equivalent of Alzheimer's disease, known as Second Childhood, a common illness among the elderly in the galaxy. The only way to save him is a shrine on Talus. The downside is that it has turned into a Wraith outpost.
September 5, 2008
Dr. Carson Beckett is called in to help a team investigating a lab that once belonged to Michael Kenmore. But soon, they realize that a group of experiments that even Michael couldn't control are hellbent on killing the team.
The Queen" 508
September 12, 2008
Primary and Commander
The Atlantis expedition has a plan to remove the Wraith's dependence on feeding to use an experimental gene therapy from Michael's database. However, in order to convince the Primary, the Wraith leader, Teyla Emmagan must pose as a Hive Queen.
September 19, 2008
Dr. Jennifer Keller is kidnapped by a runner named Kiryk. While Dr. Rodney McKay and Ronon Dex tracks them, Kiryk takes Keller to a seriously injured young girl. She must do it fast, since the Wraith have found him, and are hunting them down.
First Contact (Part 1 of 2)" 510
September 26, 2008
Dr. Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, " Todd" and a delegation arrive on the to bring forward Daedalus Dr. Jennifer Keller's gene therapy.
The Lost Tribe (Part 2 of 2)" 511
October 10, 2008
Asgard, Traveler, Wraith
As Dr. Rodney McKay and Dr. Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, " Todd" and his Wraith hijack the to find and destroy those who activated the Daedalus Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.
October 17, 2008
M35-117, Elson's planet
Balarian, Elson's people, Wraith
Dr. Carson Beckett, now a traveling doctor in Pegasus comes across a planet, where some of the villagers are refugees from Balar, a planet infected with the Hoffan drug, and destroyed by the Wraith. However, the Wraith arrive on the planet and gives the village an ultimatum, hand over the Balarians, or face destruction of the entire civilization.
October 24, 2008
Latiran, Free Peoples of Riva, Tribes of Santhal
Lt. Colonel John Sheppard's team is invited by the Coalition of Planets in order to form an alliance. However, the team is misled and is faced to stand trial, for their alleged crimes against the Pegasus galaxy. Their best chance of freedom, is the experiences of Richard Woolsey.
The Prodigal" 514
November 7, 2008
Michael Kenmore has infiltrated Atlantis with an army of his Hybrids, and closes off Stargate Operations and the surrounded levels to prevent anyone from taking it back. His plan; take Teyla Emmagan and her child to perfect his Hybrids, and to destroy the base when they're done. Meanwhile, Lt. Colonel John Sheppard, Dr. Rodney McKay and a team try to take back the city before Michael leaves with what he wants.
November 14, 2008
While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.
Brain Storm" 516
November 21, 2008
Dr. Rodney McKay reluctantly returns to Earth to witness the triumph of his rival Dr. Malcolm Tunney, but must help shut down a deadly weather device when the new technology goes horribly awry.
December 5, 2008
After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.
December 12, 2008
Neeva Casol, Jannik, Bordal
Dr. Jennifer Keller's body is inadvertently taken over by a cunning thief, Neeva Casol. While Neeva tries to escape Atlantis, Keller finds herself imprisoned with a death sentence on another planet, forcing the team into a race against time to return Keller to her original body before she is put to death.
January 2, 2009
In the city of Las Vegas in an alternate reality, police Detective John Sheppard investigates a series of bizarre murders where each body appears to have desiccated. He is soon called to Area 51, where Dr. Rodney McKay explains the situation.
Enemy at the Gate" 520
January 9, 2009
" Todd" informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a Super-hive, and wants it destroyed. However, after the is disabled, they learn that the ship is heading straight for Daedalus Earth, and they must stop it before it gets there.