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- The Circle, a secret tribunal on Galactica, decides the fate of James Lyman and other Colonials who aided the Cylons during the occupation of New Caprica.
- James Lyman (Jammer) is brought before the Circle. He is found guilty of treason for his work with the New Caprica Police, the punishment for which is death.
- Despite his pleas and an attempt to convince Galen Tyrol to spare him (as Lyman tells Chief Tyrol that he freed Cally Tyrol from the Cylon death squad (Precipice)), the Circle carries out Lyman's punishment and ejects him from Galactica by depressurizing the launch tube where he is held.
- After Lyman's execution, Tyrol talks to his wife about how she escaped. While she claims to not have thought about the incident since, Cally tells him that she thinks one of "those goons" set her free.
- On Colonial One, Laura Roslin asks Tom Zarek of his plans as the new president. Under some pressure from Admiral Adama, Zarek plans to reconvene the Quorum of Twelve, put Roslin's name in for nomination to vice president and then step down, ceding the presidency to her.
- Roslin assumes that this act requires something in return for Zarek, who asks not to be left on the outside of government affairs. For his actions in standing up to Gaius Baltar on New Caprica, she promises him the Vice Presidency.
- Felix Gaeta enters the still-damaged CIC to help with repairs to communication. Colonel Tigh yells for him to leave, accusing him of being a collaborator.
- Helo tells Tigh that Gaeta is there on the Admiral's orders, but Tigh continues to protest loudly until Admiral Adama appears. The admiral takes him out of the room to talk to him about resting so he will be ready, something that Tigh thinks he doesn't need.
- The Circle reconvenes, now under a three-day time limit to dole out justice. As they run through the cases, they eventually come to a file on Gaeta, with four of the members voting guilty.
- Samuel Anders refuses to vote and leaves the Circle, wishing to be done with killing now that he has escaped the occupation. Chief Tyrol refuses to vote if they do not have a sixth member as required for the Circle.
- Major Lee Adama speaks with his father about the Fleet's status. Major Adama notes several personnel disappearances over the past 13 days.
- As he leaves Major Adama reveals that he has lost "half a stone" in weight. Admiral Adama is not impressed.
- In the mess hall, Gaeta is treated as persona non grata, eating alone until Kara Thrace sits at his table. She talks, kindly at first, then insults him for his supposed cowardice. Gaeta counters by bringing up his status as the informant, mentioning the dog dish being flipped over as his signal to the resistance.
- The Circle brings in Kara Thrace as the replacement vote of the jury. All vote guilty on Gaeta, except for Tyrol once more.
- When Thrace questions the legality of the Circle, they show her a presidential executive order. Anders enters and requests a moment with his wife.
- The scene splits, with the other members of the Circle trying to convince Tyrol of Gaeta's guilt, and Anders trying to explain that what the Circle does isn't justice. Thrace rebuffs him, her pain from incarceration causing her to lash out at anyone, even her husband.
- Thrace tells Anders that they must separate. The Chief eventually folds and votes Gaeta guilty.
- Gaeta is captured and brought to a launch tube, told that this is an official trial under authority from the President of the Twelve Colonies, and that if he has anything to say to explain himself he should say it now.
- Gaeta replies that he has already told his story and refuses to beg.
- Kara Thrace's anger causes her to lash out at Gaeta, telling him to beg, while taunting him with the idea that he was an informant for the insurgency, and mentioning the dog bowl.
- When the Chief hears this, he reveals that Gaeta could not have known about the signal unless he was the actual informant.
- Tyrol releases Gaeta from his bonds. The other members of the Circle realize Gaeta's innocence, that he was in fact the secret source inside the Baltar Adminstration.
- Colonel Tigh stands speechless at the revelation, confused between his own certainty and the facts before him.
- Zarek reveals privately to Roslin, Admiral Adama and Tory Foster that he authorized the trials and sentences of alleged collaborators by the Circle. He claims it was an attempt to protect Roslin from having to deal with months of public trials which could destroy the unity of the Fleet through highly publicized "witch hunts".
- Laura Roslin is re-inaugurated as the President of the Twelve Colonies, and in place of her proposed public trials, issues a "general pardon" for "every human being in this Fleet". She also announces a commission on "truth and reconciliation" to record the history of the occupation for posterity.
- Still an outcast, Gaeta is reinstated in the Colonial Fleet as an officer. In the mess hall, Chief Tyrol sits with Gaeta. Both eat in silence as the other crew members are taken aback by the act.
- Gaius Baltar seems to be on Colonial One, sitting in a chair in front of Tigh, Roslin, and Admiral Adama as they talk about how there was little he could do with the situation he had on New Caprica.
- As the group forgives him, the virtual Six appears and claims the group is too lenient. Admiral Adama actually seems to hear her. Laura Roslin begins to tell Baltar how much she wants him in a provocative manner when Baltar realizes he is dreaming, waking up as Roslin kisses him.
- Baltar finds himself naked on a red chaise lounge inside an unrecognizable room. When a Cylon Centurion guard appears at the doorway, Baltar realizes that he is imprisoned in the room with only a robe to wear. The scene turns to outer space where we see several Cylon basestars surrounding a Resurrection Ship.
- A Number Three visits Baltar. She tells him that 3 days have elapsed since his arrival, and offers him a bottle of pills. She tells him that his presence on the basestar has caused a conflict between seven of the models. With three voting for him to be allowed to remain, while three vote for him to be removed. The only model that hasn't come to a consensus are the Sixes.
- Caprica Six visits Baltar and explains how wrong she was to let her feelings get in the way of her duties as a Cylon. Baltar tries to convince Six that she is more than just a Cylon and that she loves him. As she walks out he belatedly tells her that he needs her as well.
- Later, Baltar awakens to find Caprica-Six setting his clothes in his room.
- This episode marks the resumption of the survivor count which is given as 41,435, meaning that there has been a net loss of 8,115 people since the beginning of "Lay Down Your Burdens, Part II". Presumably this takes into account lives lost from the nuclear explosion aboard Cloud Nine, as well as losses suffered during the occupation of New Caprica and the subsequent evacuation.
- Laura Roslin resumes the Presidency in this episode.
- Kara Thrace (along with Anastasia Dualla) has kept her surname, unlike most other married women shown or referenced thus far (including Carolanne Adama, Ellen Tigh, Sesha Abinell, Cally Tyrol and Sharon Agathon).
- The Circle is the name used by the Bajoran Alliance for Global Unity in Star Trek: Deep Space Nine ("The Homecoming", "The Circle", and "The Siege").
- This is the second time the "Don't make me angry, Gaius. You wouldn't like me when I'm angry" threat against Baltar is used (the first time by Six, the second by Head Six and Admiral Adama).
- Tigh still has both eyes in Baltar's dream, suggesting Baltar is unaware of Tigh's injury.
- Chadwick, the woman convicted in between Jammer's execution and Gaeta's aborted sentencing, was executed - a scene discussing her death was filmed, but later cut.  Chadwick's name is spoken by Barolay. She says Chadwick is aboard the Monarch and that they have people on that ship who can take care of Chadwick.
- The Truth and Reconciliation Commission that Laura Roslin announces at the end of the episode has a number of real historical precursors, formed to bring past wrongdoing by past governments to light and thereby resolve conflicts. Those in South Africa, Peru, Chile, and Sierra Leone are actually named "truth and reconciliation commissions." Historically, such organizations tend to emerge from civil war, dictatorships, or other internal strife. In the case of this episode, the purpose of the commission is evidently to mediate grievances against Colonial collaborators during the Cylon occupation of New Caprica, while preventing more incidents of vigilante justice.
- In an original draft of the script, Gaeta was supposed to die, but writer Mark Verheiden felt that this twist would not have been believable .
- One of the names on the death list is "Justin Singh." "Singh" is a name borne by all baptised Sikh men, and is a curious addition to the spiritual parallels of the Colonies to the real-world Earth.
- A scripted and shot, but ultimately deleted, subplot of the episode featured Tory Foster secretly supplying information to the Circle (Battlestar Galactica: The Official Companion Season Three).
- As scripted, Gaeta begs for his life when he is about to be executed. Actor Alessandro Juliani instead felt that his character should accept the situation (Season 3 Companion).
- Tom Zarek's claim that his secretive and murderous policies are legal echoes US President Richard Nixon's claim that "if the President does it, it's not illegal."
- The flight from New Caprica is referred to as "The Second Exodus", implying that the "First Exodus" was from the Colonies to New Caprica.
- This is the first time viewers see the interior of a Cylon basestar. In "Kobol's Last Gleaming, Part II" only a hangar is seen when Boomer encounters her sisters.
- Lee Adama mentions that he lost "half a stone" referring to his weight. A stone is a unit of weight used mostly in the United Kingdom and Ireland that is equivalent to 14 pounds or 6.34 kg. Jamie Bamber, the actor who portrays Lee, is British.
- Galactica's living spaces and hallways appear much more crowded than in the first two seasons, reflecting the expanded size of her crew. There also appear to be civilians mixed in with Galactica's crew complement, which is likely the result of overcrowding and the loss of some of the ships during the colonization and occupation of New Caprica.
- The armor plating of Galactica is visibly damaged from the Battle of New Caprica.
- The only two humanoid Cylons to appear are Number Three and Number Six.
- On the disposition of the Pegasus crew and separated military personnel:
- Saul Tigh has resumed service as Galactica's XO. However, his experiences on New Caprica are hindering his ability to perform his duties.
- Lee Adama is performing bookkeeping work. He still wears his Pegasus uniform and commander insignia, but his position on Galactica is unclear.
- Louanne Katraine is not seen.
- Karl Agathon is working in Galactica's CIC, likely managing duties as tactical/watch officer in Gaeta's absence.
- Anastasia Dualla is not seen.
- Felix Gaeta is asked to help repair communication systems damaged during Galactica's atmospheric insertion in "Exodus, Part II". He is later seen in uniform in the mess hall.
- Galen Tyrol is back in uniform and has re-enlisted.
- Cally Tyrol is briefly seen caring for her son and asks if it is her turn "to stand watch". (Her reenlistment is confirmed in a later episode, "A Day in the Life".)
- Seelix is on Galactica as a member of the Circle, but is not seen in uniform. (Ron D. Moore indicates in his podcast for this episode that Seelix has returned as a member of Galactica's crew.)
- The glowing red strip on the wall in Baltar's room resembles the eye of a Cylon Centurion or Raider.
- Will there be an illegal organization in the Fleet that will continue where the Circle left off?
- Since Tigh has been reinstated into the Colonial Fleet, where does this leave Galactica's chain of command? Specifically, what are the roles of Tigh, Helo, and Kelly now? (Answer 1 and Answer 2)
- What of Lee Adama, Anastasia Dualla and other officers of Pegasus? How will these redundancies be dealt with? (Answer)
- Given that there are civilians aboard Galactica from the Second Exodus, and previous sabotage events that plagued Galactica prior to colonization of New Caprica, are they restricted to certain areas? (Answer)
- Has Samuel Anders become a member of Galactica's crew, or is he only allowed on board because of his relationship with Thrace? (Partial answer)
- Will any of the Circle's members or Zarek face charges, or will they be pardoned by Roslin's government for what they had done? (Answer)
- Now that the Cylons seem to have accepted Gaius Baltar, at least begrudgingly, what will happen to him? (Answer)
- What happened to those who were left behind on New Caprica?
- Which Cylon models are in favor of allowing Baltar to stay with them (besides Three, who proposed it in the first place) and which are not in favor?
- Does Caprica-Six setting Baltar's clothes on his bed indicate that the Cylons have chosen to allow him to remain? (Answer 1 and Answer 2)
- What became of Zarek's deal with Roslin to become vice president after his order authorizing the Circle came to light? Did he become vice president, or is he back on the outside? (Answer)
- How could the Circle operate in Galactica's launch tubes without William Adama's notice or, for that matter, the notice of anyone on the usually-busy hangar decks?
- Does the general amnesty apply to Baltar? (Answer)
- Are there going to be new laws outlining rules of contact with the enemy for the future?
- Isn't it becoming obvious that the survivors now need a new constitution since the current system doesn't seem to work in the environment it is in?
- With the revelation that Gaeta was the inside source, why hasn't he been recognized and welcomed as a hero of the resistance?
- Lucy Lawless discusses a humorous incident during James Callis' nude scene:
- iF: "I interviewed James Callis awhile back and he said you had an interesting reaction to his public nudity?"
- Lucy Lawless: "He was standing there, and I walked in. He was standing there holding his genitalia and the camera was on us, so it might’ve been on his back, I don’t recall. It was over the shoulder on us, and at some point he took his hand away and fluttered his hands in the air. I just about had a heart attack! [Laughs] I’ve never seen a naked man on a set ever, or a woman for that matter. It didn’t used to happen in syndication. I do have to say, “well done there, man! Congratulations! Masel Tov James!” [Laughs] For somebody who considers themselves pretty fast on their feet generally I was gobsmacked, I couldn’t continue the scene. I think it was the only time ever that I have had to walk away from a scene because I was just flummoxed."
- iF: "Well it didn’t sound like you were alone, he said one of the techies walked into a wall?"
- Lawless: "It was envy. [Laughs] It was complete envy."
- Ryan Robbins discusses throwing Jammer out an airlock:
- Robbins: Well, (lots of laughter) we were in the control room, we were in the launch bay and I actually pushed the launch button to open the hatch. You would think that maybe somebody in the CIC [noticed] that a hatch had been opened, boy oh boy, that’s a Ron Moore, David Eick question (lots of laughter) I’m going to defer to those guys along with Michael Rymer. There was so much discussion about what it would actually look like when someone goes out an airlock. These guys, “Battlestar Galactica” really try super hard to pay attention to details. We have people, you know from NASA, that you know, technical people that get phone calls from time to time saying what would actually happen. There’s a fine line between scientific fact and truth and dramatic effects for television so sometimes I think lines get a little bit fuzzy. But I’ll bet somebody out there has a great excuse has a great reason why nobody notices that airlock being opened. (laughter) but it ain’t me. I just push the button and pushed poor “Jammer” out that thing, poor guy.
- After discussing the thirteen missing persons:
- Commander Lee Adama: I've got a date with a jump rope. Hey, I've lost half a stone.
- Admiral William Adama: Keep jumpin'.
- Number Six: Don't make me angry, Gaius.
- Admiral William Adama: You wouldn't like her when she's angry.
- Tigh confronts Gaeta about his suspected collaboration:
- Tigh: Hey! Long as you're here, maybe you can help me out. I'm missing something. I lost it in detention. Since you're so buddy-buddy with the Cylons, maybe you know where it is. How about it? Do you know where my eye is?