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.
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.
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 weapons platform.
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 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.
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 hive ship.
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.
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.
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.
Sheppard's team meets a civilization about to be destroyed by a super-volcano, and is trapped there when the Stargate is destroyed during the evacuation.
The Atlantis team must decide the fate of a colony of Wraith they have turned into humans. Dr. Weir must defend her leadership when she is evaluated by the I.O.A.
Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, but discover that they may not have left Atlantis in peace.
The Atlantis team goes against orders to try and save Atlantis from Replicator control -- and to rescue General O'Neill and Richard Woolsey, who are trapped in the occupied city.
The inhabitants of Atlantis begin to suffer ill effects when the planet's whale population begins migrating to the island city, bringing an unexpected harbinger of doom.
After an Ancient device gives Rodney superhuman powers, his enhanced brilliance is checked only by his impending death -- unless he can learn how to ascend.
The team tries to relax during a mandatory day off, until an explosion leaves three people dead -- and reveals that one scientist is a walking time bomb.
Floating in deep space with the city's protective shield failing, the team must do all they can to keep Atlantis alive. A radical injury threatens Dr. Weir's life.
Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators -- but must rely on a compromised Dr. Weir to succeed.
When a group of Ronon's people enlist the team's help in raiding a Wraith weapons facility, Ronon reconsiders whether his future lies in Atlantis or with his friends.
During an off-world mission Colonel Sheppard unknowingly becomes host to an alien entity, which infects others in Atlantis and afflicts them with terrifying nightmares.
Colonel Sheppard is captured by the inhabitants of a generational ship and their beautiful leader, who wish to use his ability to use Ancient technology for their own ends.
When a virus causes amnesia in everyone except Teyla and Ronon, the Atlantis team must work together to find a cure before their memories fade entirely.
The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. The Wraith seek a new alliance with Atlantis in their war with the Replicators.
A mysterious drone crashes into Atlantis, indicating that the Replicators may have found the city. But when Elizabeth Weir appears, the team realizes that the probe is just a part of a bigger mystery.
Colonel Sheppard and Dr. McKay must protect a child princess on a pilgrimage before she can become queen, and learn that she has dangerous enemies threatening her life.
Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.
As a mysterious new illness sweeps through the Pegasus Galaxy, Teyla is convinced by a vision that the father of her child is trying to communicate with her.
Sheppard returns to Atlantis after a mission and finds the city abandoned, all systems dead -- and instead of ocean, sand dunes as far as the eye can see.
Ronon once again comes face-to-face with Tyre, one of his people who became a Wraith worshiper -- but who now claims he has broken free of their influence.
Teyla goes in disguise as a Wraith queen when Todd agrees to make a bold proposal to the leader of his alliance -- not realizing that he has other intentions.
When Daniel Jackson visits Atlantis, he and Dr. McKay discover a hidden lab that brings a new enemy knocking. The Daedalus welcomes a Wraith ally for a special project.
Sheppard races to an Ancient laboratory to save McKay and Daniel Jackson before Todd arrives to destroy a weapon that has a devastating side-effect. Daniel uncovers the identity of the hostile new species.
The Wraith arrive in a village where Dr. Beckett is working, and demand that the locals turn over a group of refugees who survived the Hoffan plague -- or the entire village will be obliterated.
While being evaluated by the I.O.A. Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Sheppard is captured and tortured by an enemy he thought was dead.
Rodney returns to Earth with Jennifer to witness the triumph of his rival, who believes he has solved the problem of global warming. But when the new technology goes horribly awry, Rodney must help shut down the deadly weather device.
After Todd's hive ship shows up over Atlantis transmitting a distress call, the team discovers that he and his crew have been stricken with a disease they helped create.