Un equipo de científicos cree haber encontrado la ubicación de la ciudad perdida de Atlantis. Se puede acceder a través de una dirección de la Puerta Estelar que conduce a la galaxia de Pegaso.

Es el cumpleaños de Elizabeth y recibe un regalo muy especial: una mujer que ha estado en estasis en un laboratorio de Atlantis durante 10.000 años y en realidad es ella misma.

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.