A team of scientists think they have found the location of the long lost city of Atlantis. It can be reached by a Stargate address that leads to the Pegasus galaxy.

There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.

Atlantis offers help to the Hoffans, who are working on a defense against the Wraith.

A team of scientists, including McKay, Zelenka and Ford, are exposed to a deadly virus. Sheppard goes after one of the scientists trying to escape.

The team is on Dagan, where they must find key stones to retrieve a ZPM. Zelenka finds out Atlantis has a deep space scanner.

McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.

Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

McKay and Zelenka come up with a plan to repair the Ancients' weapon satellite. Bates and Teyla get into a fight. He is found unconscious and badly injured shortly afterwards.

After returning to Earth for his father's funeral, John Sheppard discovers the existence of a human form Replicator loose on the population.

Sheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge.