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- The Cloud 9's lounge is under attack by terrorists who are convinced that Sharon Valerii is playing the military. The leader of this quartet, Sesha Abinell, demands that the invaluable Valerii be brought to her -- otherwise Ellen Tigh, Anastasia Dualla, Lee Adama, Billy Keikeya and others will be executed.
- Keikeya, also aboard Cloud 9, finds Dualla there. An awkward moment arises when he discovers that she is with Lee Adama. Adama leaves the two to talk, going to sit at the bar, where he encounters Ellen Tigh, who begins to flirt with him.
- Three men and a woman named Sesha Abinell lay siege to the establishment, taking the guests hostage, and sealing the area off from the rest of the ship. Abinell's husband was killed aboard the Greenleaf when the Cylons attacked it ten weeks ago, and she decides to exact vengeance.
- Before the terrorists lay siege, Lee Adama asks Ellen Tigh to come with him into the restroom. Tigh follows, thinking that Adama has invited her for a sexual tryst. But Lee Adama had predicted the situation. As a gambit to confuse the terrorists, Adama takes the dry ice from Tigh's drink and uses it to sabotage one of the oxygen sensors. In the meantime, Tigh leaves the restroom and loudly announces herself to the terrorists.
- Abinell demands that Admiral Adama and President Roslin turn over Cylon Sharon Valerii to her, seeking Valerii's life in compensation for her husband's. She is infuriated that Admiral Adama and Roslin continue to allow one of their greatest enemies to live in their midst, even caged. She believes that Valerii is compromising the security of the Fleet, and that the Cylon holocaust was due to similar Cylon infiltration of the military.
- Abinell sends one of her men into the restroom to find anyone else they haven't rounded up. Captain Adama gets the drop on him and takes his gun, taking him out, threatening to kill him if the hostages are not released. Abinell threatens to kill Dualla if Adama refuses to surrender. Adama drops the empty threat and surrenders.
- Captain Adama's small-scale sabotage works, and the terrorists demand repairs to be made to the ship's oxygen systems.
- Kara Thrace, along with a detachment of Marines, are also on leave aboard Cloud 9. They quickly plan a recon mission — Thrace disguises herself as the technician sent to repair the air system. Her job is to reconnoiter the situation and return with details.
- Thrace's cover is blown when Ellen Tigh recognizes her as one of Galactica's pilots. Thrace draws two pistols and begins shooting at the terrorists, soon aided by the Marines. Two Marines are killed, along with one of the hostage-takers. In addition, Thrace accidentally shoots Lee Adama. Thrace and the surviving Marines retreat, and the situation is only exacerbated.
- The situation prompts Admiral Adama to once again consider the value of Sharon Valerii to him. Speaking with Valerii, she reminds the admiral that she saved the Fleet five or six times. Adama asks if she would reveal the identities of other Humanoid Cylons in the Fleet. She refuses. Oddly enough, this seems to reaffirm her value to him.
- Admiral Adama agrees to give the terrorists the dead body of Sharon Valerii in return for the hostages. However, he secretly delivers the dead copy of Valerii known as Boomer. When the terrorists realize the ploy, Sesha orders the terrorist Kern Vinson to kill Anastasia Dualla. Billy Keikeya seizes one of the terrorists' guns and kills Vinson, but is mortally wounded by Vinson's return fire as Marines storm the lounge. Abinell is killed by Marines, her body falling atop Boomer's body.
- In the aftermath, Dualla stays with Lee Adama in the infirmary, promising to stay with him until he recovers. Neither notice Starbuck quietly leaving sickbay as she says this. Laura Roslin grieves the death of Keikeya, who had become "the closest thing that [she had] to family."
- Why doesn't Caprica-Sharon want to tell Adama who the other Cylons in the Fleet are, if she's been trying to show that she's helping the humans and not the Cylons?
- Possibly Sharon just doesn't want anyone to have to die, human or Cylon, and thinks that the Colonials will kill the Cylons hiding in the Fleet if she outs them. However, the Cylons hiding in the Fleet are striving to bring about the deaths of all surviving humans, so this leaves the question of why Sharon doesn't believe that capturing or killing them would prevent the deaths of an even larger number of people, perhaps the entire Fleet. She might just be unrealistically optimistic about the entire situation.
- In light of the rape in "Pegasus" and Fisk's death in "Black Market", it has been repeatedly proven that Adama doesn't have total control of the Colonial forces under his command, despite the support of the government.
- Sharon later reveals part of her motivation (in "Precipice") as being angry with herself for betraying the Cylons for Helo and her unborn child.
- Sesha Abinell's husband Ray was killed during a Cylon attack ten weeks prior to this episode. The only change in the survivor count which remains unaccounted for was between "Home, Part I" and "Home, Part II", however, those episodes must have taken place well before Ray Abinell's death ten weeks prior to this episode. His death could be offset by a birth in between episodes. Another possibility is an error in the counting.
- One of David Eick's Video Blogs is devoted to discussing the scene where Ray Abinell dies. Although the final version is a dialog-less flashback, the flashback was scripted and shot with Ray talking on the phone to Sesha, then seeing the Raider coming. He then says goodbye, hangs up, and runs down the hallway. This alternate flashback sequence is a deleted scene featured on the DVDs.
- Dualla seems to recover rather quickly from Billy's death. In fact, during much of the episode, her attention is focused on Lee Adama.
- The final scene recalls that of "Resurrection Ship, Part II", except that Thrace's and Dualla's roles are reversed.
- On Sesha's laptop, there is a list of the "Cylon modus operandi", which includes a fact that should not be known to the civilian fleet: the fact that the Cylons are attempting to breed with humans and reproduce hybrid offspring.
- Many crew members know about Helo and Valerii`s relationship, so it follows that they may also know that Valerii is carrying Helo`s child, ergo hybrid offspring.
- Another possibility is that since people have seen Valerii interacting with Adama and other members of the crew, it can be assumed that they have also noticed her pregnancy. Considering how much of the 'modus operandi' is speculation and rumor it is probable that they simply assume that the pregnancy is a hybrid.
- Among the papers in Abinell's quarters is one entitled "Can Cylons reproduce?", which was probably distributed by the press. From this it follows that speculation about the Cylons is rampant among the civilian population and that they might even have circumstantial evidence for their suppositions.
- We know it to be accurate, but for Abinell it may have been unproven speculation that just happened to be true. For example, Baltar implicated Doral as a Cylon in the Miniseries, but he had no proof at the time. We only learned later that he happened to guess correctly.
- There is a continuity error introduced when Admiral Adama and Roslin discuss the question of who might have leaked the presence of Caprica-Sharon to the Fleet. Adama fails to mention the possibility of D'Anna Biers being the source of the leak, despite his being aware of her having seen Sharon in sickbay. (Final Cut)
- Admiral Adama starts to refer to Caprica-Sharon by the name Sharon, a fact not lost on Tigh, who calls him up on it. This is a far cry from earlier episodes in which Adama referred to the Cylon as "it" and a thing.
- Who leaked out the information that Valerii is on Galactica? Was it one of Galactica's crewmen?
- Now that this information has been confirmed, thanks to the actions of Abinell and her conspirators, what kind of backlash should Roslin and Adama expect to face?
- Who will become Roslin's new assistant? (Answer) Was there a replacement groomed for the position at all previous to the events in this episode?
- Where did Abinell and her people get the weapons? Were they purchased from the Black Market?
- What were Ellen Tigh's intentions? Did Tigh purposely blow Thrace's cover, or was this accidental?
- Is the relationship between Apollo and Dee against military protocol in the same way that Tyrol and Valerii's relationship was, or have the rules on Colonial officers and NCO fraternization been relaxed? (Answer)
- Just how far does the non-association protocol even extend anymore? What is the exact nature of the non-association protocol? Is it against officers having relationships with enlisted crewmen, or even enlisted crewmen having relationships with other enlisted crewmen (i.e. preventing Tyrol and Cally from having a relationship)?
- Saul Tigh's prejudices are fully and repeatedly exposed in relation to Caprica-Valerii (e.g. describing her as a thing, objecting to William Adama's reflexively referring to the prisoner by her assumed name). Will this begin to affect the close relationship between these two in future episodes? Will it deteriorate to a point where the XO will be relieved again in relation to a decision made by Adama as he is in "You Can't Go Home Again"? (Answer)
- Why are Lee Adama and Kara Thrace on leave at the same time? Who is acting as Galactica's CAG during this episode?
- Abinell and Vincent are standing near Boomer's body when Abinell shoots it. If the Marines outside could see that she was shooting a dead body, why couldn't they shoot Abinell and Vincent when they attempted to execute hostages? If they couldn't see her, why didn't they respond to the sound of Abinell 's gunshots?
- It was kind of my choice in a way. I was kind of given an ultimatum eventually because in between the end of season one and the beginning of season two I had actually gone to LA and booked a pilot. Because Battlestar production didn’t have me under contract, I was free to go and do that. And it was their loss if the show got picked up and I wasn’t able to come back for season two. I think that was a problem they had with a few of the cast members, that everyone was a free agent after season 1, and I think that scared them a little bit. They could have potentially lost half their cast after season 1, and I think after that, they pretty much ended up signing everyone to a contract. But I’d already been cast in another show and decided to go off on my own and see if it worked. As it turned out it didn’t work, and I ended up having a two episode hiatus after episode 4. I was gone for 5 and 6, then came back for Home Pt. 1, I think it was. Or Home Pt 2, I came back for. So after that kind of gave me the ultimatum and said sign a contract for 5 years, or we kind of need to go our separate ways. And I kind of put it off and put it off, then eventually they just said “Look, we can tell you're not really committed to the show, and we can’t write story lines. So we’ve decided to kill the character." It wasn’t really a surprise, but I wasn’t expecting it to happen when it did. But I certainly wasn’t surprised that they had to do that. 
- Kandyse McClure discusses the feeling on the set regarding Keikeya's death:
- I was really sad to see Paul go. He was one of the first members of the cast to be killed and I was definitely heart sore. We don’t find out too far in advance about upcoming scripts, but the feeling on set was definitely sad. You have to take these things as they come and always be able to let go. You never know what the writers have in store or what incredible plot twists are coming up.
- Saul Tigh: You know, if people knew how much you've relied on that thing's so-called intelligence, they'd be scared out of their wits.
- William Adama: What about you, Saul? Are you afraid of her?
- Saul Tigh: You know, the truth is I don't like the way it's gotten under your skin.
- William Adama: Saul, we can't give her Sharon. I hope you know that, right?
- Saul Tigh: I know that. Against our dealing with the terrorists... if we start now, it'll open the floodgates; and it will never stop. And by the way, it's not Sharon. It's a frakking Cylon.
- William Adama: You don't think I know that?
- Saul Tigh: I think there's part of you that looks into that thing's eyes and still sees that young girl that reported aboard two years ago as a rook pilot. Well, it's not. It never was. Bill, it's a machine.
- Saul Tigh: What if they're right? What if Sharon has been playing us all, plotting our destruction with every passing day? What if the terrorists are right?
- Laura Roslin: This isn't about Sharon. It's about something much bigger than that. It's about the long term survival of the Fleet. It's about the way we conduct ourselves in all of this.