The start of this episode picks up three days after the "Exodus" from New Caprica episode. There has been a Vigilance committee group calling itself "The Circle." "The Circle" consists of Colonel Tigh, Chief Tyrol, Samuel Anders, and three others that execute Jammer for collaborating with the Cylons, and particularly for his part in the deaths of all of the civilians in the "Temple Massacre." Jammer pleads that he was only trying to help people, and tells of how he helped Cally escape from the Cylon execution. "The Circle" is unmoved; they decide that this doesn't make up for the other deaths for which he is responsible. The group executes Jammer by venting him into space through a Viper launch tube. Anders expresses his displeasure over his participation with "The Circle."
Felix Gaeta is brought into the Galactica CIC to repair its communications system, and is verbally abused by Col. Tigh for being a collaborator. Admiral Adama orders Col. Tigh out of the CIC. Kara later criticizes Gaeta for the same thing over lunch. Gaeta claims to have explained repeatedly that he was funneling information to the resistance but no one will believe him. Kara appears traumatized by her long captivity with the Cylons and is suffering from displaced rage. Her marriage seems to be under severe strain as a result. She tells him, "I just want to tear your eyes out for even looking at me". Anders gives her back her dogtag and says he doesn't want it anymore.
"The Circle" begins to discuss the possible execution of Felix Gaeta, and Anders leaves in disgust. The Chief Tyrol also threatens to quit and says that six unanimous votes are needed to approve a death sentence. Col. Tigh replaces Anders with Kara but she questions the legality of the group. Col. Tigh then shows her a Presidential Executive Order that legalizes their activities.
Meanwhile, Lee is attempting to lose weight and informs his father of a string of unexplained disappearances in the fleet. Thirteen people have vanished and all of them were known to have escaped from New Caprica.
In the absence of Gaius Baltar, Tom Zarek has become President of the Colonies. Although he knows that Admiral Adama and the military will never support him as President, he agrees to stand down in favor of Laura Roslin. He decides to reestablish the Quorum, and he nominates Roslin as Vice President, and then resigns once she is confirmed. Zarek asks Roslin if he can still play some part in the new government. Impressed by the way that he stood up to Baltar on New Caprica, Roslin offers him the Vice-presidency.
"The Circle" abducts Gaeta and prepares to execute him. They give him one last opportunity to defend himself against the charges. Gaeta refuses to beg, believing that his pleas would fall of deaf ears. Kara in a rage, physically attacks Gaeta, and demands that he beg for his life. She sarcastically repeats things he told her during her earlier verbal assault, including the "dog bowl" sign, he used to pass information to the Resistance. Chief Tyrol recognizes that Gaeta is indeed the inside source that helped the Resistance, and "The Circle" releases him.
Roslin and Admiral Adama discover that "The Circle" had been authorized by President Tom Zarek. Zarek even signed all the death certificates personally (which makes "The Circle" a death squad instead of a vigilance committee). Roslin and Adama are horrified, but Zarek is quick to point out that this had to happen and it had to be anonymously done, or else this would lead to a massive witch hunt in which everyone would accuse everyone else of collaboration with the Cylons. Then there would be hundreds of executions, many of them innocent people. He also didn't want to have her start her new term as president with this, so he decided to take care of it before she took office.
Roslin is again sworn in the President of the Colonies and in her inaugural address she declares a general amnesty for everyone, regardless of what they did on New Caprica. She intends to begin a commission to go through the fleet and record everyone's stories of New Caprica. Whether there story was good or bad, she wanted to know what they did or what happened to them for posterity. Admiral Adama leads the applause at this announcement, while ex-President Zarek shakes his head.
In the meantime, Baltar is shown as a prisoner on a Cylon Basestar, part of a large fleet (which includes a new Resurrection Ship). The Cylons are debating whether they should have brought him along since he is human. The seven models taking part in the decision of what to do with him, deadlocked three for and three against, the final decision rests with the number Sixes, who are in an emotional turmoil over Baltar's influence over them. Baltar tries to charm Caprica Six, but as the scene ends his future remains in doubt.
After Roslin's announcement of a general amnesty, Gaeta is shown in his Colonial military uniform, dining alone in the mess hall. It becomes evident that despite the amnesty, he is still being shunned due to his involvement with the Baltar-Cylon administration. Chief Tyrol enters the mess hall and makes a conscious decision to join Gaeta at his table.