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- With an impending supernova, the Colonials and Cylons see their time running out as they endeavor to unlock the secrets of the Eye of Jupiter. Meanwhile, Number Three executes her plan to know the faces of the Final Five and Sharon Agathon tries to get her daughter back.
- Others in Galactica's CIC, particularly Colonel Tigh and President Roslin, become increasingly agitated and shocked as Admiral Adama continues issuing orders to arm and launch several nuclear missiles at the Temple of Five. He instructs Colonel Tigh to enter his launch codes as Adama does the same on his command console.
- On the algae planet, Lee Adama's resistance movement is preparing. However, the Major and Samuel Anders are still fighting over saving Kara Thrace after her Raptor crashed from a Cylon missile attack. When Anders angrily proposes that he will shoot Major Adama if Thrace is dead, Adama snaps, "If she's dead, I'll let you," no longer attempting to hide his feelings about the downed pilot. Their impasse ends when Adama calls his wife, Lieutenant Dualla, and orders her and Sergeant Fisher to attempt to rescue of Starbuck.
- In the previous episode, the Colonials warned that they would destroy the continent where the ancient temple resided if the Cylons attempted any landing there. Six Heavy Raiders are now heading to the planet, and Adama is intent on showing the Cylons that he is not bluffing.
- The Cylon basestar command detects Adama's continued missile preparations and become visibly worried that Adama will indeed destroy the Temple. Each of the available models immediately agree to a recall, except for the Number Three model, who defies the command group's consensus, and refuses to recall the last Heavy Raider.
- Galactica notices the recall of all but one of the Heavy Raiders, which gives Admiral Adama a moment to reconsider. After several tense moments, Adama rescinds the launch order and orders his battlestar to stand down.
- The Cylons are relieved as well, but after the Three in the command room leaves in satisfaction, the others realize that the Cylon, a race predicated on consensus and not defiance or distinctive personality clashes, have a serious problem. A Cavil voices that the Threes are out of control, and that a decision regarding their actions must be made, sooner rather than later.
- In their quarters, Helo is angry, saddened and unable to talk his wife, Sharon Agathon into letting him take a Raptor or another transport to rescue their daughter, Hera, from the Cylons. In the end, both embracing, Helo shoots his wife to force her consciousness to download and resurrect on the Cylon Resurrection Ship so that she can attempt the rescue alone.
- Galen Tyrol and his team continue deciphering the glyphs inside the Temple of Five for discerning the location of the Eye of Jupiter, believed to be an important artifact that gives further data on the road to Earth. Their investigation does not go well, although Chief Tyrol believes he is close to translating the writing.
- Admiral Adama and President Roslin meet with Helo and question his wisdom in the Agathons' rescue attempt of their daughter. Adama is concerned that the Cylons may gain critical tactical data from their defected former colleague, whether she volunteers it or not. When Roslin criticizes Helo, he angrily reminds her that if she hadn't stolen their daughter, none of them would be in this situation.
- Dualla and Sergeant Fischer make their way to Starbuck's location, but are soon attacked by a Cylon sniper. Fisher is killed, and Dualla scrambles, weaponless, along an alternate path to Starbuck's location.
- Starbuck has survived her crash relatively unhurt except for severe burns on her hands. The pain is so severe that Thrace hasn't sufficient dexterity to inject herself with a morpha shot for the pain. When she hears a noise outside, however, Starbuck suppresses the pain long enough to raise her sidearm at her Raptor's open door.
- Dualla appears at the entrance, and Thrace admonishes her for not making her presence known. After administering a morpha shot, Dualla proceeds to assess the Raptor's damage. She tells Thrace that she was ordered to "bring Starbuck to Apollo," a choice of words meant less to describe the rescue order and more to describe her pain over the "secret" affair between Adama and Thrace.
- Sharon Agathon downloads successfully. Through fortune or design, it is Caprica-Six who greets her at the Cylon rebirthing tank. Six tells Agathon that her child is ill and her condition is worsening, to the confusion of the Cylons.
- On the planet, Major Adama's team have set a bomb kill zone in a ravine which all attacking Cylon forces must walk through.
- When the Centurions spot the trap, Jean Barolay is forced to detonate it before the Cylons completely enter the blast radius.
- The explosion removes the lower torso of one Cylon, but it, along with the two undamaged units, return fire. The Colonials destroy the legless Cylon, but lose one of their own in the firefight. Having lost their only chance to hold back a Cylon advance, they begin a retreat to the highlands of the planet to await rescue.
- Major Adama calls Chief Tyrol and orders the immediate evacuation and destruction of the Temple of Five lest it fall into Cylon control. A reluctant Tyrol orders his team out and soon follows, with a detonation cord reel to the G-4 packs in his hands.
- Dualla continues to repair the damaged avionics from cannibalizing datacord from the ship's communications system. When Thrace's pain increases, Dualla (with an apparently less-than-cordial "bedside manner") stabs Thrace's leg with another morpha injection. As she drifts into a sedated delirium, Thrace confesses her confusion about the romantic entanglements she is in. Dualla slaps the pilot both in annoyance and in an attempt to keep Thrace focused on a major problem: the former petty officer on Galactica is not flight-trained and cannot fly the Raptor, while Thrace's injuries make it impossible for her to fly.
- Gaius Baltar, the "D'Anna" Three, and a Cavil prepare to enter the Temple. Baltar's virtual Six appears to remind him, despite Three's feelings, that Baltar himself and not Three is the "chosen one" who is meant to activate or access the Temple's secrets.
- Reunited with the other Colonials at a safe distance from the Temple, Tyrol is reluctant to detonate the Temple's explosives. When Major Adama wrestles the detonator away from Tyrol and activates it, nothing happens. Unknown to them, Cavil, Three, and Baltar have removed the detonator caps from the G-4 immediately after they entered the Temple.
- Chief Tyrol and the team see the atmosphere ripple and pulsate as the star begins its nova. The star's corona (or its effect on the atmosphere above the Temple) takes shape to form a likeness of the circular multicolored starburst-like mandala that decorated the Temple. Tyrol quickly realizes that the star itself is the Eye of Jupiter. The Colonial team goes to investigate.
- The algae planet's home star has made a helium burst of its outer atmosphere. The star is going nova. Everyone, Cylon and Colonial alike, have less than an hour to escape the system.
- Sharon Agathon and Caprica-Six arrive at Hera's room, where Agathon's Galactica predecessor, Sharon Valerii, is tending the child. Valerii is visibly angered at Agathon's presence. When Agathon picks up her crying daughter, the child's cries cease momentarily. Caprica-Six curiously realizes that, while both Agathon and Valerii are biologically identical, Hera is able to recognize her mother.
- Agathon's human first-aid training recognizes that Hera's stomach is too firm, suggesting a possible intestinal blockage. When Valerii comments that the Cylon doctors detected no such problem, Agathon reminds her that the Cylons have no pediatric care experience, having medical experience only with the adult humanoids of their kind.
- Agathon tries remind Valerii of her love for Chief Tyrol and Admiral Adama, but the former "Boomer" denies her past and reject any possibility that humans and Cylons could co-exist, remembering only too well the events on New Caprica.
- Agathon pulls Caprica-Six from Hera's bedside and tells her that, for Hera to survive, she must see a human doctor -- which means returning to Galactica. When Caprica-Six seems reluctant to go through with this, Agathon tells her that the child is so important to the Cylon God that their God would never forgive her for letting child die. Meanwhile, Valerii grows increasingly unstable and physically threatens to break Hera's neck. Agathon pleads for Hera's life as Caprica-Six manages to knock out Valerii. To prevent her from coming to, Six breaks Valerii's neck.
- Caprica-Six finally agrees that Hera (and others that come after her) are too crucial to the future of the Cylons (and, by implication, the Colonials) for her to let the child remain in the hands of the Cylons. She helps Agathon escape to Galactica by way of one the Cylons' captured Raptors.
- Inside the Temple of Five, Baltar quietly notes a Colonial sidearm left behind while Cavil and Three examine the structure. When the virtual Six points out the only mandala on a raised section of the floor, Baltar notes it, and Three gravitates to it as well.
- The light created by the supernova is channeled through the central spire's crystalline mechanisms and activates a beam of light on the floor's sunburst.
- Cavil attempts to stop the Three from using the beam, and tells her he knows that she's not doing this to find Earth, but to seek the forbidden identities of the Final Five. He points a gun to shoot Three, but Baltar shoots and kills the Cavil from behind.
- Three walks into the light and immediately sees the vision of the five she's seen before. Unlike before, however, she is able to discern the specific faces. Three stands in front of one face (not visible to viewers) and immediately recognizes it, apologizing to the being for past transgressions saying, "You . . . Forgive me I . . . I had no idea," before the vision abruptly stops.
- Dualla manages to fly the Raptor into space, with Starbuck's guidance.
- Admiral Adama orders an immediate Raptor rescue of everyone on the planet after the Cylons baseships retreat to escape the pending nova shockwave.
- Three's eyes cloud as she apparently suffers fatal damage from the Temple's vision mechanism. Baltar catches her as she falls.
- She says to Baltar, "You were right." (It is possible she still thinks she is speaking to one of the Final Five.) Baltar tries to get Three to tell her what she has seen; specifically, Baltar wants to know if she saw his face among the image of five beings. However, Three dies before he gets an answer.
- Baltar drops Three's body and stands in the mandala, attempting to see the vision himself. However, the Temple's illumination from the star has ceased, and so has the vision mechanism. As Baltar prays to God to help him, he finds the barrel of a Colonial sidearm resting on his head, and Chief Tyrol is holding it. The Chief sarcastically greets the deposed president and pistol-whips him unconscious.
- Raptors are seen flying away from the planet and to Galactica. The battlestar is under full sublight power, escaping from orbit while buying time for the Raptors to land and for the battlestar to prep for an FTL jump. The nova shockwave is approaching rapidly.
- Galactica barely escapes the remains of the algae planet as the star's shockwave tears through its system. She momentarily reels out of control due to the leading edges of the shockwave reaching her before her escape.
- Chief Tyrol and his group unload a body bag from his Raptor onto a gurney. He stops the gurney and discreetly shows Colonel Tigh that Baltar is inside, alive but unconscious. Tigh orders Tyrol to have Baltar taken to the brig.
- Samuel Anders and Kara Thrace reunite. Lee Adama and Dualla, each on opposite sides of Thrace and Anders, see this as well. Adama moves to embrace his wife. Thrace and Adama's eyes meet over the shoulders of their spouses. Sharon and Caprica-Six arrive as well and Colonel Tigh orders Caprica-Six taken to the brig while Helo and Sharon take Hera to see Doctor Cottle for treatment.
- In a briefing, Tyrol, Lieutenant Gaeta, Roslin, Admiral Adama and Helo analyze the new supernova and compare it to the Temple's mandala, realizing that the Thirteenth Tribe must have wanted anyone who followed after them to look for this mandala, or specifically, another supernova. Gaeta finds the remains of a similar supernova 13,000 light years away, in a cloud of gas know as the Ionian nebula.
- Helo is fascinated by a picture of the temple's mandala. He makes his way to Kara Thrace's quarters and asks if she had any photos of her old apartment on Caprica.
- He finds a painting that Thrace had made on one of her apartment's walls. It is very similar to the temple's mandala, which was created 4,000 years before.
- When Thrace sees this, her mood darkens. She tells Helo that she had doodled this symbol often as child because she liked the patterns, having no prior source for the symbol. She relates something that a Leoben Cylon told her over a year before: Thrace had a destiny, and, according to Leoben, it was already pre-written.
- On the Resurrection Ship, D'Anna-Three downloads successfully to find a Cavil sitting next to her tank. Cavil notes curiously that at least Three will not have to go through the process of resurrection again, and explains why.
- The other Cylons believe that Three's delusions of messianic intentions have revealed her as an inherently flawed design. Three counters that it is not wrong to seek one's own purpose, that the search for who and why the Cylons were built is an important task.
- The decision has been made to box the entire model. Three tells Cavil that he and the others will see the faces of the Final Five one day, but with a press of a button by Cavil, Three and all of her kind are deactivated. The scene expands to show other Cavils performing the same task on hundreds of other resurrection tanks.
- Prior to the airing of this episode, James Callis revealed that Gaius Baltar returns to Galactica in this episode.
- According to Ronald Moore's podcast, the image in Kara's apartment was a symbol that the actress had decided to paint before the actual shooting occurred.
- Moreover, the ground battle was originally shot in more structured manner. Bradley Thompson spent time on location to work out the tactics used by both sides to create a realistic engagement. However, that didn't translate on screen. Partly because of the many closeups, most of the terrain looks the same, making it impossible to get an impression of the location of each fire team. As a result the battle was heavily cut and changed in the editing room, to at least make it the most exciting.
- The cigar box from which Helo takes the photo of Starbuck's apartment is the same one she picked up there in "Valley of Darkness".
- The Eye of Jupiter and Starbuck's artwork bear a strong resemblance to the Ring Nebula. However, the order of colors from center to edge is different: blue, white and red for true color images of the actual nebula; blue, red and yellow for the Eye. The actual nebula is also a bit more oval in appearance while the Eye is nearly circular.
- The leitmotif "Sense of Six" which normally is played for appearances of Baltar's inner Six is played for D'Anna Bier's death scene in Baltar's arms. It is not played, however, for Inner-Six's appearance within the temple.
- Dualla was initially meant to drag Starbuck over ground to safety, but this has to be scrapped to due budget constraints. Their scenes in the Raptor were not filmed on location, but on a soundstage (Battlestar Galactica: The Official Companion Season Three).
- The five figures in white bear a striking resemblance to the occupants of the Ship of Lights from the Original Series.
- If the device which triggered Three's vision was a viewing mechanism which was programmed when the temple was built, her recognition of one of the figures in white would mean that there is some substantial connection between whomever the Temple of Five was dedicated to and the Cylons.
- If the five priests are actually the Final Five, then the Cylons are using ancient genetic templates as indicated by their susceptibility to a virus that the rest of the human race was immune to.
- The basestar command apparently does not require consensus of all models, or need not have them to have a representative at the command center. Simon and Number Five are not seen during this episode. Of course, since there are only seven models at this time, four models casting the same vote is decisive. This is exactly what happens when Six, Eight, Leoben and Cavil vote in favor of recalling the Raiders.
- Despite no longer being XO, Helo is still included in high-level briefings. This may reflect another facet to his current duties aside from mere Raptor jockeying (this may also be supported by the fact that he is more often seen in uniform rather than flight suit or fatigues currently).
- The tension between Athena and Boomer reaches a climax when Athena attempts to rescue her daughter. It has become clear that Boomer, like Athena, was presented with two choices, but unlike Athena, did not choose the path that led to forgiveness. Both Eights have suffered persecution from the Colonials. Athena, however, partly due to her love for Helo and Adama, chose to forgive, while Boomer allowed the failure of New Caprica to push her over to the belief that humans and Cylons should go their separate ways. However, Boomer does not seem to fully belong into Cylon society either, maybe being distrusted because of her association with humans. Given the events of "No Exit" and season 4 including Boomer's awareness of the identity of the Final Five at this time, her relationship with Number One may have to do with this.
- Boomer comments that Cavil believes that the Cylons aren't supposed to have children. This is unsurprising, given that model's lack of religious faith and belief that the Cylons shouldn't be emulating humans.
- Caprica-Six continues her defiance against Cylon society by choosing to believe in a possible new future between Cylons and humans. This particular Cylon, ever since her deception that led to fall of humanity, has consistently shown increasingly human traits. Like her decision to save Anders by killing a Three to pave the way for a possible new future between Cylons and humans, her decision to kill Boomer to save Hera echoes those same beliefs.
- The rescue of the people on the algae planet occurs in an extremely short amount of screen time. This is reminiscent of the short amount of screen time that was given to Galactica retrieving her fighters before jumping away from the Battle of New Caprica. As noted in prior podcasts, sometimes there just isn't enough time available in each episode to show everything in detail, which makes it necessary to compress events.
- The survivor count decreased by one at the start of this episode counting the loss of one of the civilian combatants during a gunfight on the planet's surface.
- Hera, according to Caprica-Six, is able to distinguish her mother from the other Eights. Whether this indicates that Hera inherited a Cylon ability is yet to be seen. At the very least, on an emotional level, Athena and Hera have a mother-daughter bond that does not exist with Boomer.
- According to the podcast, Boomer's jealousy and rage developed over time, especially when she became Hera's primary caretaker. When it became apparent that Hera was not responding well to Boomer, she slowly developed a resentment towards Athena, because according to the Cylons, Hera existed because of God's true love. This implicated that the reason that Boomer and Tyrol were not able to conceive was because they didn't have true love between them. This, and Hera's response once Athena arrives, eventually led to the rage Boomer showed.
- After the initial stand-off ends when Adama decides not to nuke the planet, the defiant Three model states that no one would do such a thing over just one ship. However, ironically, that is exactly what Adama himself fears in "Hero" when he believes that the one recon fighter that crossed over into Cylon territory was what eventually led to the genocide of humanity.
- Ironically, the boxing of the Threes may actually make consensus harder to come by in the future. Now that the number of known Cylon models is an even six, a true deadlock is possible.
- This eventually does happen in Six of One, when the question of whether to "lobotomise" the Raiders after they "malfunction" in Crossroads Part II ends in a vote of 3-3.
- The removal of the Threes also exaggerates the uneven gender ratio of the known models, from 4 male:3 female to 4 male:2 female.
- Boxing the entire line of Threes prevents any of them from accessing D'Anna's memories to learn what she discovered.
- Now that Athena has resurrected into a new body, her susceptibility to the Cylon virus is in question. Athena was immune because her child gave her body human antibodies to the disease (A Measure of Salvation). In a new body that has never given birth, a possible reintroduction of the virus could be lethal to Athena. Conversely, Athena's immunity could have become a programming element that downloaded along with the rest of her consciousness, just as the lethal virus could follow the consciousness of an infected humanoid Cylon to a Resurrection Ship, potentially inoculating all Cylons against the virus.
- Three's conversation with Cavil at the end of the episode reveals that the humanoid Cylons do not know who programmed them or why.
- Who does Three recognize as being one of the Final Five? (Answer)
- Why are the identities of the Final Five kept a secret? Why would the other seven Cylon models not know the identities of the Final Five, and why would the Number One model want to prevent the others from learning about them? Do some or all of the Cylons not want to know and why would this be so? (Answer #1, #2, #3)
- Does a mechanism exist to revive boxed Cylons, given that their memories and thoughts still exist in cold storage? (Answer #1, #2, #3)
- What is the connection between Starbuck and the Eye of Jupiter? (Partial Answer)
- What is Starbuck's destiny? (Answer #1, #2, #3)
- What will President Roslin and Admiral Adama do with Baltar now they he is back in their custody? (Answer)
- Will Roslin and Adama's relationship sour now that Adama knows of Roslin's involvement with hiding Hera? (Answer)
- What will happen to Caprica-Six now that she is on Galactica? (Answer)
- Do the Cylons realize the significance between the mandala and the nova? (Partial Answer)
- With the temple destroyed, what is the significance of Baltar being the "chosen one" rather than Number Three? (Answer #1, #2, #3, #4).
- Why was the temple dedicated to the five priests who served a separate unnamed god? (Partial Answer).
- Are the five priests the Final Five? (Partial Answer)
- Who did program the humanoid Cylons and why? (Answer)
- What does Three mean when she tells Baltar that he was right? Is she referring to something else that he said to her earlier? Or does she still think she is speaking to one of the Final Five?
- Is the empty drape for a god, the chosen one or somebody else?
- Now that Athena is in a fresh body, does this mean she is no longer immune to the virus that killed the Cylons on the basestar?
- Although it has been established that Resurrections occur with other Cylons present to help the resurrected Cylon get through the process, how did Caprica-Six know to be present for the revival of Athena (why not a Three, or Cavil, etc.)?
- Information from the podcast:
- "We had talked a lot about what this moment was, in terms of how did the mes— how did they— how does she see the final five and what is the message that is left to Galactica and the Colonials about where Earth is. At first we went out of our way to avoid doing the well of lost souls, which is— y'know you're standing in the well of souls and— Indiana Jones in the first Raiders of the Lost Ark movie, and the sun comes in a certain position and the light shines in. And we tried various versions of all kinds of tech things happened with the supernova that sent messengers or sent arrows and— not literal arrows, but metaphorical light beams in a certain direction— and ultimately, in the cut, we said "No, it's the well of souls." The light comes in, and the light shines down and it takes you to a certain spot. 'Cause it works. And that's what you go with." 
- "Here's— I like this little bit of business with Baltar's body coming back in a body bag, which I believe was— if I'm not mistaken— was something they made up on the set. Michael Rymer and James came up with this whole thing about hiding him in the body bag, and I heard about this afterward, in fact, I got a call from the studio, from Todd Sharp, who's the head of production at Universal, (laughs) called me and said "Are you aware that Baltar comes back to the Galactica in a body bag?" And I said "Yeah! Yeah! Yeah, that was a co— Yeah. Yeah, we talked about that, it was a complicated decision. And we'll talk about that more later.", and then I hung up on him. "Baltar comes back— what the fuck are they doing down on the set!?" And then I called Rymer, and "WHAT?!?", and he said— he explained it to me, and I said "Oh. Well that's smart." (laughs) Sometimes you just have to let— you have to be— you have to be willing to let them be smart, because they come up with some really nice stuff, and that was a really nice way of getting Baltar back aboard Galactica without having to play a whole big thing of hoopla, of bringing him back in chains or something."
- I loved that episode too! I have a great deal of respect for Katee and her work. I was really excited for the opportunity to finally get a real meaty scene with her. Contrary to what the scene is about, there was actually a lot of laughing going on… Katee is hysterical! We definitely don’t let what’s going on in the writing affect the quality of our work environment.
- The Admiral prepares his ship to unleash its nuclear arsenal:
- William Adama: Mr. Gaeta, disable launch and warhead safeties on tubes four through ten.
- Felix Gaeta: Safeties disabled. Warheads … are armed.
- Adama: XO, please input your firing code.
- Saul Tigh: These nukes will obliterate anything or anyone within twenty clicks of the Temple.
- Adama: I know.
- The Cylons react to Number Three's (D'Anna Biers) insubordination:
- Cavil: That is not a good sign, my friends.
- Number Eight: She defied us. Defied the group.
- Leoben Conoy: It's not about the Eye of Jupiter. It's about her.
- Caprica-Six: It's like we don't even know them anymore.
- Cavil: We may have to so something about this. We may have to do it, sooner [rather] than later.
- Chief Tyrol finds Gaius Baltar standing alone in the Temple of Five:
- Tyrol: Welcome home, Mr. President. (Pistol-whips Baltar, knocking him unconscious)
- Number Three (D'Anna Biers) to Cavil in the Temple of Five:
- Number Three: This is my destiny. To see what lies between life and death.