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.
- Leaders from the human populations of many worlds have formed an official alliance and extend an invitation to Lt. Col. John Sheppard and his team to represent Atlantis at their next meeting.
But on arrival, the team is immediately detained in a concrete cell and Sheppard is brought before three council members Kelore of Latira, Shiana of the Tribes of Santhal, and Dimas of the Free Peoples of Riva to stand trial for crimes against the indigenous peoples of the Pegasus Galaxy.
Richard Woolsey, meanwhile, receives a visit from Myrus, a representative from the new coalition of planets, who advises him that Sheppard and the others are being made to answer for the deaths of millions throughout the galaxy.
Outraged, Woolsey demands that Myrus bring him to his people, confident he can take on their defense and secure their freedom. But it quickly becomes clear that even Woolsey's formidable legal and diplomatic skills may not be enough to save the Atlantis expedition from a guilty verdict.