The story picks up three days after the exodus from New Caprica. A Vigilance committee-like group calling itself "The Circle" and consisting of Colonel Tigh, Chief Tyrol, Samuel Anders, Diana Seelix, Charlie Connor and Jean Barolay execute Jammer for collaborating with the Cylons, and in particular for his part in the deaths of a score of civilians in one of the "Temple Massacres." Jammer pleads that he was trying to help people, and tells of how he helped Cally Tyrol escape from the Cylon execution squad. The Circle is unmoved, however, and decides that this doesn't make up for other deaths for which (they feel) he is responsible. The group executes Jammer by venting him into space through a Viper launch tube. Anders expresses his disillusionment over his involvement with The Circle.
Felix Gaeta is brought to the Galactica CIC to repair its communications system, and is verbally abused by Tigh for being a collaborator. Admiral Adama orders Tigh from the CIC. Starbuck later criticizes Gaeta for the same thing over lunch. He claims to have explained repeatedly that he was funnelling information to the Resistance, but no one believes him. Starbuck, herself, appears traumatized by her long captivity with the Cylons, and is suffering from displaced rage. Her marriage to Anders is 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 any more.
The Circle begins to discuss the possible execution of Felix Gaeta. Anders, supported by Chief Tyrol, argues that there is no hard evidence against Gaeta, and that The Circle is merely guessing as to what Gaeta may or may not have done. When the other members disagree, Anders quits The Circle in disgust. The Chief also threatens to quit the Circle, and says that six unanimous votes are needed to approve a death sentence. Tigh replaces Anders with Starbuck. Starbuck questions the legality of The Circle, until Chief Tyrol shows her a Presidential Executive Order that legalizes The Circle's activities.
Meanwhile, Apollo informs his father of a wave 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. Knowing that Admiral Adama and the military will never support him as President, he agrees to stand down in favor of Laura Roslin. He will re-convene the Quorum, nominate Roslin as Vice President, and then resign once she is confirmed. He 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 on deaf ears. An angry Starbuck physically attacks him, and demands that he beg for his life. She sarcastically repeats things he told her during her earlier verbal assault, including the "dog bowl" signal that he used to pass information to the Resistance. Chief Tyrol quickly realizes the significance of the statement and demands to know what Gaeta revealed to Starbuck. Gaeta then repeats what he told: that he had used the yellow dog bowl as a signal that there was important information in the dumpster.
Tyrol then realizes the mistake "The Circle" made and releases Gaeta. When the others complain of Tyrol's actions, Tyrol revealed what he had just realized: that Gaeta was the source that leaked information from within, and it was because of him that the Circle gained the list and other important information, and to a larger extent, the reason why humanity is back under the protection of Galactica. The Circle reacts in horror, shame, and embarrassment over what they were about to do, and Gaeta states that he did all he could to help and leaves.
Roslin and Admiral Adama finally learn of The Circle, and that it had been authorized by (still) President Tom Zarek. Zarek even signed all the death certificates personally (which makes the Circle a death squad instead of vigilance committee). Roslin and Adama are horrified, but Zarek points out that this had to happen quickly and anonymously. Zarek feared that there would ensue a massive witch hunt in which everyone would accuse everyone else of collaboration, and there would be hundreds of executions, many of them wrongful. He claims that he didn't want to mar her presidency with this, so he decided to take care of it himself before she took office.
Roslin is again sworn in as president, and in her inaugural address she declares "a general pardon for every human being, in this fleet", 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 what they did or what happened to them, both good and bad, for posterity. Admiral Adama leads the applause at this announcement, while ex-President Zarek looks away.
Baltar, meanwhile, is 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's human. Of the seven models taking part in the decision of what to do with him, the issue is deadlocked three for and three against. The final decision rests with Caprica-Six. Baltar appeals to Caprica-Six, but as the scene ends, his future remained in doubt.
Following Roslin's announcement of a general amnesty, Gaeta is shown in his Colonial military uniform, dining alone in the mess hall. It is evident that despite the amnesty, he is still 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.