On Atlantis, Woolsey informs Sheppard and his team that they've been invited to attend a meeting of civilizations throughout the Pegasus Galaxy. McKay is less than impressed given they have no technological advances. Everyone agrees and they take a Stargate to the designated planet. They're escorted to a chamber and gas is pumped in, rendering them unconscious.
The team wakes up in a cell without their equipment and men arrive to escort Sheppard to the Council. He's informed that he'll be representing Atlantis on behalf of charges filed against the expedition. They've been accused against crimes of the people of the galaxy.
Major Lorne reports back to Atlantis informing them Sheppard's team has been moved from the village where they arrived. Woolsey orders him to search the area with more men.
The Council explains that they are meeting in a secure location and note that the Atlantis expedition is responsible for the death of over two million people. They note the Wraith were in hibernation when they arrived but Sheppard explains that the Wraith attacked them first on a culling mission. They rescued their people, encountering a Queen and killing her. As she died, she warned that the other Wraith would awaken. The Council notes that due to the early awakening, several civilizations have been rendered all but extinct. Sheppard refuses to play along but they warn that they have many other charges and if he refuses to defend Atlantis, they'll be found guilty automatically. They acknowledge that they can't jail the Atlantis expedition, but they can cut off all trade. If Sheppard and the others are found guilty, they'll be exiled on an uninhabited planet.
Back in the cell, Sheppard explains what happened and they figure they're on a different planet in an underground bunker. McKay insists that they are innocent but Teyla notes that lives have been lost because of their presence. Sheppard says they have no choice but to play along.
Myrus, a representative of the Coalition, comes to Atlantis to meet with Woolsey.
Sheppard returns to the Council and they bring up the plague caused by Michael. They have Sheppard testify that they conducted research to solve the Wraith problem by converting them back to human. Michael was the first test subject and they tried to convince him he was a human soldier, but he soon discovered otherwise and escaped. Eventually they destroyed his ship but don't know for certain that he's dead.
Woolsey informs Myrus that the arrest was unwarranted but Myrus warns that they've been making decisions unilaterally affecting the entire galaxy. Woolsey has Myrus confined to reconsider but the latter warns that such a decision will confirm the Coalition's opinions. Woolsey has him locked up nonetheless.
The Council brings up the Genii plan to battle the Wraith and Sheppard explains how the Genii tried to ambush them and take their weaponry. He notes that the Genii couldn't have carried out their intended plan without Atlantis technology.
Lorne has been unable to find out anything about the missing team and Woolsey doesn't believe the entire galaxy has turned against them. He decides on a plan and goes to see Myrus with a proposal.
Sheppard testifies that they've had some military success against the Wraith, in part by turning them against each other and in part by using Ancient technology. The Council is unimpressed, noting that he has no evidence to substantiate his testimony. They're interrupted when Myrus arrives with news. The Council calls a recess and has Sheppard taken back to his cell… where Woolsey is there with the others. He informs them he'll be taking over their defense and has a plan to win the trial. He believes his legal experience is sufficient to deal with tribal elders.
Woolsey goes before the Council, who ask him about the Replicators. He explains what the Replicator are and why they're attacking human worlds to deny the Wraith their food supply. Woolsey is forced to explain that Atlantis is the ones who activated the Replicator code to attack Wraiths. He notes that their choice cost them Dr. Weir but the Council is unimpressed, noting that the humans put the Replicator "tools" into process. Woolsey tries to argue that in balance more Wraith were wiped out but one of the Council members, Shiana, notes that her people were wiped out and Woolsey's attitude proves that Atlantis is unconcerned about the lives lost.
Back in the cell, Woolsey notes that one of the Council members is connected to the Genii and is helping to set the Genii up to take control. They still don't have a viable escape plan and Woolsey decides to win unfairly now that he knows what they're up against.
Woolsey meets with the Genii-faction Council member, Kelor. He tells Kelor that he's backing the wrong horse and offers him their military support, and they want Kelor to represent them within the Coalition.
Woolsey comes before the Council for the final accusation, that they're conspiring with the Wraith. He explains how "Todd" and Sheppard escaped together and they've been working together ever since even though they don't trust him. Together they managed to defeat the Replicators. The Council prepares to recess but Woolsey asks to make a final statement. He points out that the Wraith are in disarray but it won't last forever and they'll need Atlantis as an ally. Shiana asks for an immediate hearing: Shiana votes guilty, Dimas votes innocent, and Kelor considers the matter…
Woolsey returns to the cell to inform them they're free to go. Back on Atlantis, Sheppard and Woolsey share a drink and cigars and Woolsey explains that they had to commit themselves to a stronger day-by-day involvement in politics. Sheppard figures that they're there to make a difference, and they can worry about it later.