We begin the episode with a somber funeral ceremony for Cally. Chief Tyrol delivers a powerful speech about how he's lost his way without her and how he laments her loss.
As Chief steps down from the dais, Roslin leans over and whispers to Admiral Adama how she likes the type of service given to Cally. Adama responds that it is not his taste. Roslin then says "I know. But I want you to know what I like," making it clear she is referring to her impending death and how she would like her funeral to be handled.
The service ends and everyone begins to leave expressing their condolences to Galen, but Chief continues to stare after the departing Tigh and Tory, even ignoring the goodbyes of others (Lee Adama).
We then find ourselves with Col. Tigh, as he inquires as to the condition of Caprica Six, who has been held prisoner onboard. Tigh wonders out loud as to how the Cylon can keep its sanity in the confined cell, to which a Marine says, "Probably turns its brain off. Frakkin' toaster."
Tigh then enters Caprica Six's cell and informs her that her requests have all been denied once more. Six begins to inquire as to why Tigh keeps coming to see her every day. Tigh begins to leave, worrying that perhaps Six may suspect he's one of the final five hidden Cylons due to his constant visits, when suddenly he no longer hears Caprica Six's voice. He turns to see a vision of his deceased wife Ellen in Six's place.
It's revealed to us, through quick camera work and editing, that only Saul is seeing this vision of Ellen superimposed onto Six, no one else.
Tyrol is now at home staring blankly at his son, Nicky, when Tigh and Tory both come into the room and confront him on his behavior bringing attention upon themselves.
Saul wonders if Galen is going to get his son to stop crying to which Galen replies unemotionally that the child probably needs to be changed. Seeing that Tyrol is in no condition to function, Tigh goes to check on Nicky. Tory seizes the opportunity and begins to tell Tyrol that he need not feel guilt as they were "made to be perfect."
Tyrol looks up at Tory in disbelief. He asks her how she can live without guilt. She responds coldly to simply shut it down, which Tigh overhears. Chief looks up at Tigh asking if they're still going to be the men they were before, to which Tigh replies an agreement and tells Tory to be quiet. Tory responds that while that may be true, they should recognize themselves for what they are and seek that hidden potential.
Tigh begins to tell Tyrol about how his grief is human and it not end any time soon, even saying how he will see her everywhere he goes. He then simply states to feel what he needs to feel, but to stop putting them at risk.
We then find Tory waking Gaius Baltar from his sleep pulling his hairs out one at a time. She begins to force herself on him as she speaks of pain and pleasure mixing together. Gaius is quite unnerved as usual whenever he's being cornered.
We then begin to see quick flashes of a weapon-toting militia/brigade converging on Baltar's location as Tory steers the conversation towards Baltar's teachings that the One God forgives all sins. She makes the argument that if all is forgiven, it wouldn't matter what you did. Baltar is quite taken aback by that remark as he sits up and states "that would more than imply that we're perfect."
The raid begins as gas canisters are deployed and armed men storm Baltar's followers' quarters. They brutally attack those in their way and leave when Baltar is nowhere to be found and before the true military discovers their presence aboard. Tory looks around and finds Baltar hiding behind an elevated railing.
Chief is working on repairs for a craft when he begins to have visions of his life, good and bad, with Cally. Time seems to blur for a moment as Tyrol finds himself several hours later surprised by the pilot of the craft asking if the work was completed. Chief responds, "Yes." When taken out for a flight however, Racetrack's ship malfunctions and she is forced to make an emergency crash landing.
We cut to Baltar pleading for military aid in protecting him and his followers safe from attacks. Head Six appears and prompts Baltar to read the "old text" graffiti left behind.
The terrorist group calls themselves the "Sons of Ares." Baltar deduces that this is a direct result of people being angered by his teachings of the One God.
Head Six then begins to goad Baltar further as she prompts him to start a conversation with an elderly woman nearby stating that "the old gods die hard. Even amongst your followers." Baltar soon discovers that not all of people are willing to give up their old religious ways fully just yet, as it's revealed that the old woman held a medallion of the god of healing from the Twelve Gods pantheon. Six then states that "the old gods are fighting back."
It's soon discovered that Tyrol forgot to replace a crucial component in the spacecraft. At first angered, one of the flight crew begins to confront Chief about his error but quickly backs-off when he realizes he'd be yelling at a grieving man. Chief takes offense to this act of pity and demands to be treated like anyone else. When Racetrack says he's only human, Tyrol explodes at everyone within earshot yelling "Don't tell me that! Tell me I frakked up!" as they all walk away.
Gaius Baltar is now confronted by Head Six. She tells him how there is only room in a person's heart for one love. Gaius' teachings of the One God, or the Twelve Gods of Kobol. Gaius, in a very Christ-like way, then asks why he can't simply be a man. Six then tells Baltar that should he win this war of the hearts, he would be like a God himself, to which Baltar states "it's not about that," as he looks on to those around him. Head Six begins to smile as he continues saying it's about the people.
Baltar demands they all stop their works of repair. "This is unacceptable. We have been targeted, because of what we believe, by those who answer to faceless gods, that bear no relevance in our world. They want us to be afraid. But I am tired of being afraid. The time's come to make a stand and that time is now." Baltar then leads a charge into a religious gathering, in direct alliteration to the biblical narrative of Jesus and the money changers, before he is taken away by a security detail.
Admiral Adama meets Roslin in the sickbay as she finishes a blood test. Adama is carrying a new book entitled "Searider Falcon." Adama states it's his favorite book and admits he's never read the end, much to Roslin's surprise. Laura probes deeper and learns that Adama was saving the ending because he didn't want it to be over. Laura says "Maybe I should do that."
As Adama escorts Roslin, he informs her of Baltar's recent arrest. Roslin says it's his revenge for the attack against him and that Baltar continues to provoke dissent. Adama is quick to point out that the fleet does not need a religious war. The two continue to discuss how to handle Baltar since Roslin wishes to keep him close-by but does not want to make him a martyr. Roslin then states that she's going to visit Baltar because she wants him to see her.
Tigh returns to Caprica Six's cell and begins to ask questions about how Caprica Six deals with the knowledge that she's killed millions of people. He then probes her if she can feel it or if she can simply "turn it off." Six responds that Tigh pretends they are different but he should know better. At first perturbed that she's deduced his secret, Saul orders the guards to raise their weapons, but when it's revealed that Six was implying that she's more human than machine, made of blood and veins, not switches and relays, he begins to see his deceased wife again.
Tigh visibly becomes engrossed in his vision as his now dead wife's image begins to offer him forgiveness. He orders the guards to leave when the vision breaks again and he's face to face with Caprica Six asking him to open himself to her.
Roslin visits an already beaten up Baltar in the brig. She admits to him that her health has been failing once more and that her hair is now a wig. It seems the two drop all the pleasantries and formalities of their rivalry and are talking frankly to one another in this scene, as Roslin proposes that so long as Baltar leads a quiet life she would die a quiet death, but should Baltar act up she's clearly threatening to make his life misery since any penalty for a broken rule or law is nothing compared to her impending death. She coldly states that she's "no longer in the mood to indulge him and that's all."
Admiral Adama tries to console Galen at Joe's Bar by telling him that he would be more than willing to accommodate Chief's needs for more or less work. Tyrol begins to hallucinate that Adama is insulting him, calling Cally a coward for killing herself and little Nicky a half-breed abomination, for a split moment before the illusion breaks and Adama states "she was a good woman." This was the final straw in Tyrol's already fragile mental state. He begins a slow monotone rant about how if she was a good woman, Adama would never have threatened her (as he had in previous episodes) when suspected of betrayal or of being a Cylon and that he's thought about hurting her himself.
Before Adama can discourage him from going any further, Tyrol asks the question of "How many of us ended up with the people we really wanted to be with? We got stuck with the best of limited options. And why? Because the ones we really want, we really loved are dead, dying or turned out to be Cylons and they didn't know it. If Boomer had..." and then explodes with a tirade to the world "I didn't know. So I buried my head in the sand and I took it and I settled. I settled for that shriek, with those dull vacant eyes. The boiled cabbage stench of her. And why? Because this is my life. This is the life I picked and 'it's fine.' But you know what, it's not! I didn't pick this life. This is not my frakkin' life."
Tired of seeing everyone glorify his dead wife Chief continues until he's finally brought to halt by a stunned and angered Admiral Adama who demotes him to specialist and orders him to re-assignment in the morning, leaving Tyrol alone at the bar.
In the Quorum meeting Roslin attempts to fast-track a resolution to limit public gatherings. She intends to use the new law as a means to keep Baltar's followers from socializing as a means of both keeping their presence and religious gospel from spreading and a means to controlling Baltar. Having insulted Lee previously as a mouthpiece/spokesman and other delegates in the past with her bulldozing political tactics, Lee stands up for what is right as he claims he can't allow this latest Presidential order to stand. The other delegates all begin to agree that this order is too wide and could be used against many religions, which troubles them. Roslin angered by their hesitation, then states that the Quorum should remember what Baltar did with political power and that they should be afraid of what he would be capable of with blind religious faith before leaving the room frustrated.
We return to Tigh as he once again discusses with Caprica Six how she copes with the burden of a million deaths. Once more in the guise of his vision Ellen, Tigh hears words of how the pain and anguish of lives lost taught the machine the true meaning of death. Six says she loved Baltar more knowing he could die at any moment, breaking the Ellen illusion Tigh had been seeing.
The vision of his dead wife proclaiming her love for Gaius Baltar enrages Tigh. He orders the monitoring station and the room to be cleared so he can be alone with Six. She says pain is the key to removing all anguish and guilt and learning who we truly become. She melts into the Ellen persona once more, removing Saul's eye patch. She then proceeds to beat Tigh senseless.
Gaius returns to his quarters only to find armed guards outside his complex. They refuse to allow him and others into their homes because of Roslin's new social gathering laws. Even when one person offers to leave so that Baltar can enter, the guard refuses to co-operate.
Head Six appears to Baltar and prompts him to ignore the guard and try entering anyway for the good of the faith. As the guard repeatedly beats Baltar down, Head Six picks up Baltar's limp frame off the ground literally dragging him back into the guard's way like an invisible puppet master. Lee Adama then rushes in and demands the guard stand down since the Quorum has voted down the presidential order restoring the right of assembly. When Lee tells Baltar he didn't take this action to help him, Baltar cryptically responds that he did it because "your God compels you."
Roslin is joined once more by Admiral Adama in Doc Cottle's sick bay and is found ranting quietly about Lee's inability to comprehend the pragmatic dangers around him. Admiral Adama says Lee is doing what he thinks is the right thing, to which Laura responds, "sometimes the right thing is a luxury."
Adama reads a passage from the book to Roslin. "I wasn't afraid to die. I was afraid of the emptiness that I felt inside. I couldn't feel anything. And that's what scared me. You came into my thoughts. I felt them. It felt good."
We cut quickly to Saul begging for more punishment and possibly death from Caprica Six, when she backs away shocked saying "No. I made a mistake. This isn't what you need." She slowly reaches down and kisses him on the lips.
We hear Gaius delivering a sermon to his followers, intercut with quick shots of the Demetrius and her personnel, as they listen to him preach about how something in the universe loves him whom he decides to call God and how God loves them all and can be found in each of them. He urges them to love their faults like God does. He looks over at Tory, who had provided him the key to his religious war as he exclaims that they must all love themselves since they are "perfect," and God only loves that which is perfect. Head Six is smiling and standing beside Tory as Lee Adama leaves the room, scared of what he has allowed to thrive by following his conscience.