- For the artifact contained within The Temple of Five, see: Eye of Jupiter.
- The Fleet makes a stop at a planet and discovers the location of a religious artifact that may further lead the way to Earth—for both the Colonials and the Cylons.
- The Fleet is mending its wounds from its passage to the algae planet. The harvest proceeds well and is into its 14th day, and appears to be closing up shop.
- Kara Thrace flies from Galactica to the harvest camp in a Raptor, intentionally creating more noise than usual. Lee Adama is managing the harvest operations with his wife, Anastasia Dualla.
- When Major Adama leaves to greet Kara Thrace, Dualla's face barely hides her disappointment and frustration at Adama's hasty departure.
- Major Adama greets Thrace with an admonishment of her piloting, but his comments are very brief; the two pilots embrace and passionately kiss.
- Adama wants he and Thrace to stop hiding their feelings and divorce their respective spouses. Thrace reminds him that marriage in the eyes of the gods is a sacrament; she has made a vow she will not break. Adama reminds her that their repeated secret encounters would be frowned on by the gods as well. Adama becomes frustrated, Thrace holds her position, and the two are left trapped in their feelings.
- On a basestar, the little human/Cylon hybrid, Hera, is crying and is not well. Gaius Baltar is awakened by her cries and visits the child, who is attended by the Number Eight known once as Sharon Valerii.
- Galen Tyrol is part of the harvest team. He is repeatedly distracted by something which apparently only he can sense, and keeps looking out towards the unexplored hills beyond the harvest site. Samuel Anders, also working on the harvest, comments that the algae harvest tastes as badly as it smells. Tyrol jokes that the algae is "breakfast, lunch and dinner until we can find a hot-fudge planet."
- After sensing something strange one time too many, Tyrol leaves the harvest camp and begins a trek to a mountainous area. He discovers a door--not a naturally-carved one, but a rectangular door, apparently constructed by human hands.
- Tyrol enters the door and walks through a passageway into an immensely large domed room, carved from within the mountain. In the center of the room is a center spire that reaches high into the structure. The spire is surrounded by five pentagonal obelisks. The center spire has ancient tribal carvings at the bottom, as well as illuminated crystalline pillars atop it. Tyrol, the son of a priest and an oracle, has a fair idea of what he has discovered: The Temple of Five.
- Carbon dating of the temple indicates that is is approximately 4000 years old, which matches when the 13th colony left Kobol in search of Earth.
- Laura Roslin discusses what she knows with Tyrol over wireless about this special temple as it is told in the Sacred Scrolls in Admiral William Adama's quarters. But before they can digest the information further, they are alerted to four basestars that jump into orbit of the planet and move towards the Fleet.
- Admiral Adama orders the civilian Fleet to escape to emergency jump coordinates, but leaves Galactica behind; Adama does not want to repeat the situation on New Caprica, where he retreated with the remains of the Fleet and abandoned the colonists there. Adama chooses to stay to protect his harvest team until they can escape. He and Roslin also agree that, if the Temple of Five has a marker to Earth, they must not let the Cylons take it.
- However, very uncharacteristically, the Cylons do not attack. In fact, they request communications with Adama. The voice that Adama hears is not a welcome one: It is Gaius Baltar's.
- The Cylons request a meeting on Galactica to discuss the Eye of Jupiter. The Number Three copy that Baltar calls D'Anna, a copy of Cavil, Baltar, and the Number Eight copy once known as Sharon Valerii board the battlestar under heavy Marine guard.
- The virtual Number Six in Baltar's mind warns him that, while he may feel like he has returned home, he cannot stay: The Colonials would "toss (him) into an airlock and have a party."
- On the way to the meeting, Sharon Agathon recognizes the Eight copy as the former "Boomer" Valerii. Colonel Saul Tigh denies her entry into the meeting. The two Eights are left outside the doorway, facing each other with mutual looks of contempt and curiosity.
- The two sides meet, with Admiral Adama taking point as the lead speaker. Roslin stands behind, refusing to acknowledge Baltar's greeting or his presence.
- Baltar attempts to take the initiative in an attempt to serve as a mediator, but this infuriates Roslin so strongly that she leaves the meeting.
- Adama receives the Cylon's terms: Leave peacefully so that they can gather the Eye of Jupiter, and they will not attack. Cavil, with a sardonic face, adds the surrender of Baltar to the terms as well, to the former president's and Three's shock, "to sweeten the pot."
- Boomer-Eight tells Sharon Agathon that Hera is alive, but unwell, on their basestar. Agathon refuses to believe her.
- Admiral Adama is not amused by the Cylon's deal. Close to Three's face, Adama states his terms: Galactica will lay waste to the whole continent, destroying the planet's treasures with his nuclear arsenal should the Cylons attempt to land on the planet. The two sides depart in a state of détente.
- Admiral Adama manages to get an order to his son of the situation and to destroy the site if the Cylons invade before the Cylons jam all wireless communications.
- Major Adama instructs Samuel Anders to organize fireteams to defend against a probable Cylon incursion. Anders, also realizing what Adama has been doing with Thrace, is very angry and initially refuses to oblige until Thrace asks him to comply.
- Cally and Galen Tyrol speak in the temple. He tells her of how he was annoyed at his parents and their worship. Cally sees reverence on his face, despite his general mood of disbelief.
- Lieutenant Felix Gaeta has conducted some scans of the star system of the algae planet. He warns that the sun of this system is in danger of becoming a supernova very soon. Gaeta, who normally is as secular as his commander, finds it very strange how the Cylons and Colonials arrive at this one place at this time just before the planet's imminent destruction. Adama notes that the "higher powers" at work appear to have a strange sense of humor.
- The basestar command, with Baltar in attendance, discuss their plan to get the Eye. Cavil feels that annilihation of Galactica is the best option with the standoff (given that they are machines that can wait out humanity for years, or even millenia, and find Earth eventually).
- D'Anna, without consulting the other Cylons, has solely initiated the jamming of Colonial communications, and has already sent a Heavy Raider with a squad of Centurions to the planet as the basestar fleet jumped in, successfully avoiding Colonial detection. This action confuses the others, particularly Caprica-Six.
- D'Anna notes that, as soon as the Centurions recover the Eye, the other Cylons can destroy Galactica.
- The Centurions on the planet are seen connecting additional materials to their back as they march away from their ship.
- The Colonials, with Anders at the lead, plan out their defense on the planet. One team will manage ammunition distribution, another team will create tylium mines.
- As the harvest team-turned-point defense teams leave the tent, Major Adama compliments Anders for his honest, to-the-point direction to the group, indicating that Anders would make a good officer. Anders scoffs at Adama's compliment, implying that he knows what Adama and Thrace have been doing. When Adama tries to object, Anders tells Adama not to insult his intelligence, as he is aware that Adama is not that only one that Thrace has enjoyed sexual company with.
- On the basestar, in the Hybrid's room, D'Anna-Three is savoring the opportunity to see the faces of the Final Five Cylons--"maybe the face of God himself." The Hybrid notes, in her quizzical manner, that the "five lights of the apocalypse" and the "sins" will be revealed only to the "chosen one," lifting her head and staring directly at Baltar as she says "the chosen one" repeatedly. D'Anna's eyes are closed and is not aware that the Hybrid is addressing Baltar.
- Caprica-Six enters and questions D'Anna's intentions. D'Anna dismisses their three-way relationship as she tells of her plan to leave with Baltar to discover the secrets of the Temple. Six is visibly hurt at being left behind.
- The planet team begin their final preparations, led by Dualla. With wireless jammed, she notes how hardwired observation points are to be created to warn of any Cylon advance, with Starbuck's Raptor taking point with directions to fly to the nearest observation point to relay any sightings. Thrace's annoyance at Dualla's precise direction leads to some catty replies by Thrace, which Dualla ignores.
- As the observation teams take their positions, Starbuck begins her recon flight. As she turns along a ravine, she spots the Centurion emplacement and is immediately fired upon by the Cylon's missile battery. Starbuck tries to evade and successfully manages to relay that she found Centurions before her Raptor is struck by a missile. With the controls on fire and visibility lost, Starbuck screams as she keeps her hands on the flight controls and fights for control of the Raptor. The Battle of the Algae Planet begins.
- As President Roslin explores what little is known about the Temple of Five from the Sacred Scrolls, in particular, the five priests for which it was built, Admiral Adama interrupts her, telling her of Boomer's return and asking if the story of Hera's faked death was true. Roslin admits the truth. When she tries to explain the reasons why, Adama abruptly leaves in anger.
- Adama tells the Agathons of Hera's discovery, and both are incensed. When Helo argues how painful it was for them and how Adama should know the pain of the moment, Adama reminds him that, unlike his son, their child is still alive, and that they should be grateful for that. Sharon Agathon glares at Adama and says she wants to see her child, implying a greater intention.
- Major Adama reports to Anders that Starbuck's Raptor has gone down, but also tells him that a rescue mission is out of the question; they haven't enough manpower to rescue Thrace and defend their position.
- Six Heavy Raiders leave a basestar towards the planet.
- Galactica sees the Heavy Raiders on DRADIS immediately. Tigh feels that this is a test to see if the Colonials are bluffing. Roslin believes that they were bluffing until Adama orders Louis Hoshi to arm of a series of missile tubes, each containing a nuclear missile.
- As Anders argues for Thrace's rescue, Lee Adama explodes in defense of the mission, arguing the point that he has known and cared for Thrace for much longer than Anders, who tells Adama he is going after his wife. Adama's troops hold Anders at gunpoint.
- Unaware how events are escalating around and above him, Chief Tyrol illuminates the carved writings of the Temple with his flashlight and reads the inscriptions, trying to locate the actual resting place of the Eye. At one point, his flashlight's beam moves close to the target-shaped symbol in the center of the central spire.
- The basestar command detects the radiation signature of the missiles as Galactica targets the Temple.
- Adama authorizes the release of the missiles.
- Writer Jane Espenson revealed that this episode was originally titled "Eye of Zeus." In the podcast for this episode, Ron Moore explains that "Eye of Jupiter" just sounded better than "Eye of Zeus" and thus it was changed.
- This episode, whose teaser clocks in at just over 11 minutes, has the longest teaser of any episode thus far, narrowly beating out that of "Lay Down Your Burdens, Part I".
- The outdoor sequences on the algae planet were filmed near Kamloops, British Columbia. 
- According to the podcast, the interior of the Temple of Five is the same set, an abandoned factory, as the large room on Ragnar Anchorage where Doral is left behind in the Miniseries.
- This episode was screened in movie theaters in six cities (New York, Atlanta, St. Louis, Chicago, Dallas and Los Angeles) by TV Guide as a free promotional on December 14, 2006 one day before the United States airing. The source was a digital copy with no commercials. In at least two cities (Chicago and Los Angeles) writers from the show held a Q&A session after for fans. Also in at least two cities more than one screening was held. 
- In reality, the eye of Jupiter, also known as the Great Red Spot, is a circular gaseous thunderstorm that has marked planet Jupiter's surface for more than 300 years now. The spot is twice the size of Earth and it is Jupiter's most prominent feature being visible also from the Earth.
- In Act Three, the Hybrid quotes the opening lines of the satirical folk song "Plastic Jesus".
- At least eighteen people perished as a result of navigating through the radiation field of the star cluster. Most of these casualties are likely the skeleton crews of the Adriatic and the Carina and one of them is Kat.
- This episode ends the debate whether Admiral Adama knew about President Roslin's secret plan to hide Hera ("Downloaded", "Exodus, Part I") -- he did not know.
- When the baseships arrive, the Fleet jumps away, while Galactica stays in orbit of the planet throughout the duration of this episode and the next. So, in essence the Fleet jumped away without Galactica to follow them, and is vulnerable to attack at their rendezvous coordinates.
- The DVD release of this episode includes an alternate scene of Roslin's confession to Adama about Hera. In the televised cut, Adama gets up and walks out of the room while Roslin is in the middle of explaining her motivations for hiding Hera and lying to her parents. In the deleted sequence, however, Adama does not walk out of the room--instead, he goes into the head, removes his uniform jacket, and begins shaving. Roslin follows him and, uncertainly, finishes explaining her motivations before admitting "Bill, I don't know what you want me to do here. Should I leave? Should I stay?" Adama simply asks her for a towel and, without any apparent anger or bitterness, tells her that he wants to let Sharon and Helo in on the secret because "no one should have to live with losing a child." This may explain why subsequent episodes do not show any tension between the two over this issue, despite the apparent anger with which Adama storms out of the room in the televised cut. In addition, Adama predicts that Athena and Helo will want to get their child back, which is what Athena subsequently indicates.
- Caprica-Six and D'Anna Biers's dialogue indicates that they have been intimate with each other as well as with Baltar.
- This is the first episode showing Cylons and humans negotiate rather than instantly shoot each other (other than Baltar's unconditional surrender on New Caprica).
- It also the first time the Cylons use their "human" names on the basestar when not speaking with Baltar. D'Anna Biers is named by Caprica-Six and another Number Three. Cavil's name is used by Three.
- Coincidence (and destiny / predestination) seems to be a major theme with this episode: the humans and Cylons show up at the planet at the same time; the temple is discovered by Tyrol, son of a priest who revered this place; the planet is orbiting a star that will go supernova within days.
- Galactica has acquired at least four more nuclear warheads, bringing the total to at least seven; beginning the series with five and using one to destroy a basestar (Kobol's Last Gleaming, Part II) and another being detonated by Gina Inviere on Cloud 9 (Lay Down Your Burdens, Part II). In the podcast, Ron Moore suggests that Pegasus is the source, but the number of nuclear warheads is still limited.
- When the Hybrid speaks of the Chosen One, she looks directly at Baltar, not Three, who has her eyes closed.
- Kara Thrace's explanation of marriage as a sacrament is similar to the principles of the Roman Catholic Church. In this religion, a marriage between a baptized man and woman is one of the seven sacraments of the faith. A sacramental marriage cannot be dissolved, but only reviewed later to determine if the marriage was valid at all. If the marriage is invalid, an annulment is allowed. This suggests, by extension, that Thrace and Anders have had dedication ceremonies (the Colonial equivalent of baptism) if such a requirement is needed by the gods.
- The tylium planned for the mines could come from three possible sources: Starbuck's Raptor, the harvest camp's power generators, or reserves kept for the Raptors and other ships servicing the harvest camp. If it was taken from Starbuck's Raptor, this supports the high energy yield of the fuel that, at the same time, would not sacrifice the Raptor's flight ability.
- Now that Baltar seems to have some purpose again, he has become more attentive to his grooming, finally trimming his beard.
- Did Kara Thrace survive the crash of her Raptor? (Answer)
- What is the Eye of Jupiter and how does it point the way to Earth? (Answer)
- How will the Agathons knowing their child is still alive affect their relationship with Adama? (Answer)
- How will Adama finding out Hera is still alive affect his relationship with Roslin? (Answer)
- Is there a connection between the Temple of Five and the five missing Cylon models? (Answer #1, #2)
- Who is the "Chosen One" that the Hybrid speaks of? (Answer)
- What consequences will Number Three's actions have within Cylon society? (Answer #1, #2)
- Will there be further confrontations between the two "Sharon Valerii"-type Eight models, as seen in the passageway tirade between Boomer and Athena? (Answer #1, #2)
- When did Boomer go over to the Cylons' way of thinking? In this episode she clearly doesn't seem to think of herself as human anymore like she did in "Downloaded". (Answer)
- Does Dualla know about the affair between Apollo and Starbuck? (Answer)
- Did Adama inform Athena and Helo that it was the President who ordered the secret adoption of Hera? (Answer)
- How did Tyrol find the Temple of Five?
- Possible Answer due to revelations in No Exit: The whole thing about the blocked memories may explain how Tyrol was able to sense and find the Temple of Five: he'd been there before on his way to the Colonies so the location was in his blocked but not erased memories. They may have subconciously guided him there as he was pretty close by.
- How much truth is there to Anders's claim of Kara Thrace's chronic infidelity ("You think you're the first?")?
- Were the Cylons really willing to hand Baltar over to the Fleet?
- Why does Biers feel that Caprica-Six cannot accompany her and Baltar?
- What is the Fleet doing without the presence of Galactica?
- Who or what is "The One Whose Name Cannot Be Spoken" whom the Five supposedly follow? Is this a reference to the Jealous God, who may or may not be the "one true God" of the Cylons?
- What are the "sins" of the Five that the Hybrid speaks of?
Jane Espenson discusses the original name for "The Eye of Jupiter" and references to it in "The Passage:"
- "When I wrote this episode, the upcoming episode was already well along, and it was called 'Eye of Zeus.' So all the dialogue in my episode reflected that. It got changed to Jupiter later, and I don't know why. It's always hard to get names to legally clear. All you need is one guy named Zeus who lives in North Hollywood and Standards and Practices is all over you to change the name. (deadpan) That's probably what happened."
- The Cylon baseship requests to speak with Admiral Adama:
- Adama: Put it through speaker. This is Admiral Adama.
- Baltar: Admiral. I can't tell you what a genuine pleasure it is to hear your voice. This is Gaius Baltar.
- Six: Feels like old times, doesn't it?
- Baltar: Can't believe how much I actually miss this place.
- Six: You know you can't return. They'd toss you out the nearest airlock and then throw a party.
- Thrace: Can I make a suggestion you won't like?
- Adama: Do you make any other kind?
- The Cylon representatives, aboard Galactica:
- D'Anna Biers: The weapons are hardly necessary.
- Cavil (sarcastically, clasping his hands): Yes. Exactly. We come in peace.
- The Hybrid, giving more obscure prophecy:
- Hybrid: The five lights of the apocalypse rising, struggling towards the light... sins revealed only to those who enter the temple... only to the chosen one... the chosen one... the chosen one...
- D'Anna Biers: The Five await me. Gaius, I'm so close to knowing the truth!
- Hybrid: Look into the eye to know thyself...look into the eye to know thyself...
- During a meeting between Laura Roslin and Admiral Adama with Baltar and the Cylons
- Roslin: The less this man says, the better this will go.
- Baltar: Wait a minute. If it wasn't for me the Cylons would've blown you out of the sky two seconds after we'd arrived.
- Roslin: (to Adama) I think you can handle this alone. . . if you can stomach it.
- Caprica-Six confronts Baltar and Biers about their secretive behavior
- Caprica-Six: I'd like to think that we three have shared something, transcended the barriers that separate people, and yet somehow, the more time goes on, the more I find myself on the outside looking in.
- Baltar: Well, that's not the case at all, is it? Because, we three, we're integral, we're part of...
- Biers: We're finished.
- As the Cylon representatives walk into the conference room
- Cavil after seeing Sharon Agathon in a uniform: "Oh, look at that, should we salute?
- "Yeah, well... it's breakfast, lunch and dinner until someone finds a hot fudge planet."