After a series of run-ins with the Wraith, the team begins to suspect their Athosian allies of having a spy in their midst.
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Sheppard and the team visit a world where no one is over 24 years old -- because of a ritual suicide practice they believe keeps the Wraith at bay.
The team finds a world whose people are on the brink of a discovery that may make them immune to the Wraith feeding.
Efforts to open trade relations with a species called the Genii turn sour when the team discovers their new "allies" have ulterior motives.
McKay's efforts to harness the energy of an alien planet's atmosphere allows for a return trip to Earth -- but the team may not be able to return to Atlantis.
When a massive storm threatens the city, Atlantis is evacuated -- only to be taken over by the team's newest enemy.
Major Sheppard plays a dangerous game of cat and mouse with soldiers who have seized control of Atlantis and taken Weir and McKay hostage.
Nearly a third of Atlantis's residents are infected with a deadly virus that causes hallucinations and death, forcing a lockdown of the city.
The team finds a paradise world that would make an ideal sanctuary for those fleeing from the Wraith, but the local inhabitants believe their goddess will not permit it.
A woman is found in suspended animation in Atlantis, and the team is shocked to see that it is Dr. Weir herself, who tells them of her trip 10,000 years into the city's past.
The team searches for a valuable Zero Point Module rumored to be hidden on the planet Dagan -- but their new allies have motives of their own.
With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones.
Plagued by terrifying nightmares, Teyla begins to recall a time when she and her father were captured by the Wraith and subjected to disturbing experiments.
With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital ...
All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.
The Daedalus arrives to defend Atlantis from the Wraith onslaught, but it may not be enough when the team discovers that an even larger armada is on the way.
The Daedalus is infected by a Wraith computer virus, while members of the expedition hope to return to Earth.
Sheppard and his team attempt to locate Lieutenant Ford, only to find themselves captives of a former soldier who is being hunted by the Wraith.
A run-in with a Wraith Dart leaves the consciousness of a precocious Atlantis security officer trapped in Dr. McKay's mind.
The Atlantis team finds a culture that lives in relative safety from the Wraith, because they hand over their criminals to the Wraith -- and crash-land in the volatile penal colony.
McKay puts the team at risk when he tries to perfect unfinished Ancient technology that wiped out a civilization. Ronon Dex discovers that he is not the lone survivor from his world.
The team discovers a young Wraith girl who has been raised by a human, and is in hiding from the people of her human village in fear of her life.
Colonel Sheppard begins to undergo a disturbing physical transformation after being exposed to Beckett's anti-Wraith drug.
When the team finds an Ancient warship adrift on the edge of the galaxy, its crew still alive, Colonel Sheppard enters their virtual reality stasis to communicate with them.
The team is captured by the missing Lieutenant Ford, who is now leading a group of young men who are taking the Wraith enzyme -- and who wants the team's help in a suicide attack against a ...
Colonel Sheppard and his team find themselves prisoners of the Wraith following Ford's attack on a hive ship. Dr. McKay goes to great lengths to help them.
Sheppard finds himself on a planet where time passes more rapidly, with no way to contact his team or return to Atlantis.
When an operative of the Trust plants a bomb in Atlantis, the team must find a spy within their own ranks before the Wraith arrive and discover the city.
When Dr. McKay is trapped underwater in a sinking Puddle Jumper, his only chance for survival may be an hallucination of Samantha Carter.
The team finds a world that possesses Ancient defense technology, where Colonel Sheppard finds himself a pawn in the rivalry between the heirs to the throne.