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.

It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.

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.

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.