Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.

Michael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The other expedition members are very concerned about his well-being as he seems different.

Dr Weir finds herself on Earth where, to everyone else, the Atlantis Expedition was just her delusion.

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.