The story of Stargate Atlantis follows the cliffhanger episode on Stargate SG-1's seventh season finale "Lost City", where SG-1 found an outpost made by the race known as the Ancients in Antarctica. After the events of Stargate SG-1 season eight premiere "New Order", the Stargate Command sends an international team to investigate the outpost. Soon, Dr. Daniel Jackson discovers the location of the greatest city created by the Ancients, Atlantis. The story unfolds when the members of the expedition encounter the Wraith, the race that defeated the Ancients ten thousand years ago.
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.
During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors.
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.
Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.
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.
With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.
The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.
An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.
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.
While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator -- who is now on the loose.
McKay, Carter, and Keller are trapped in an underground chamber while on an off-world mission, with no apparent means of escape.
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.
The team is shocked when an old friend, believed to be dead, miraculously returns to them. Teyla plans an escape from Michael's captivity.
After a conflict with Michael leaves several Atlantis personnel trapped, Colonel Carter leads a rescue mission.
When an alien organism incapacitates Dr. Keller, the team seeks help from an old friend recently revived from stasis.
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.
The team boards the Daedalus when it shows up abandoned in orbit, only to find themselves skipping through parallel universes.
The city of Atlantis becomes host to the minds of disembodied Replicators, led by someone very close to the team.
Rodney McKay is stricken with a mental affliction that robs him of his knowledge and memories, causing him to revert to a childlike state.
Sheppard and Beckett join a team investigating a hidden Wraith laboratory where Michael has been conducting genetic experiments.
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.
Ronon and McKay join Dr. Keller on an off-world errand of mercy, and must track her through the forest when a Runner kidnaps her.
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.
A new coalition of human worlds puts the Atlantis team on trial for their alleged crimes against the Pegasus Galaxy.
The team fights to retake control of Atlantis when Michael infiltrates the control room to take Teyla's child and destroy the city.
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.
Dr. Keller's body is taken over by a cunning thief, while Keller finds herself imprisoned with a death sentence on another planet.
In the city of Las Vegas, Detective John Sheppard must solve the case on a long string of unusual murders -- perpetrated by a Wraith in hiding.