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- Chaos is rampant as paramedics try to save Commander Adama's life after he is shot, and Galactica is accidentally separated from the Fleet.
- Note: This is part one of a two-part episode. Part two is "Valley of Darkness".
- Moments after Commander Adama is shot by Boomer, Captain Adama yells out for Doctor Cottle. Since he is not on board, Dualla searches for him throughout the rest of the fleet.
- Medics arrive and take Adama to sickbay. Meanwhile, Boomer wonders what has happened, and in response, Tigh has the Marines take her to the brig.
- Also, Tigh has brief flashbacks back to the time when he first meets Adama.
- Gaeta then detects a basestar on DRADIS, preparing to ambush the fleet. Dualla locates Cottle on board the Rising Star; however, he cannot be shuttled to Galactica as Tigh is forced to order the fleet to make an emergency FTL jump to escape the Cylons. When asked about the survivors on the surface of Kobol, Tigh replies by saying that the people down there will have to wait.
- Meanwhile, Apollo is taken to the brig alongside President Roslin who is given news that Adama has been shot. Apollo asks Corporal Venner to remove his cuffs, but is denied.
- After the rest of the ships in the fleet have escaped, Galactica performs its own jump to safety; however, when Gaeta reads DRADIS there are no other ships nearby. They have somehow lost the fleet, and are stranded in space, alone.
- Gaius Baltar and Number Six are inside the Opera house where they look down at their child. Baltar wonders if the baby is metaphorical, but Six tells him that the baby is real and she is the mother and Gaius the father. The child may not be born yet, but will soon be. Six then asks Gaius if he wishes to hold her. Hesitantly, he agrees and moves to do so when he wakes realizing it was just a dream and mutters "am I the father?"
- Baltar and the rest of crew of Raptor 1 are still on the surface of Kobol, near the ruins of the city. Seelix is giving the injured Socinus some serisone to help him breathe and Cally presses Baltar to carry something along with the others when they make their way to the tree line and await rescue.
- While checking the supplies, the team hears a sonic boom, and realize that a Cylon ship has entered the planet's atmosphere and they must find cover immediately. Although Chief Tyrol feels they have enough time to ensure they have all of the needed supplies before moving out, Crashdown overrides him and leads the group to hide among the trees.
- On Galactica, Tigh changes his blood-soaked clothes while Ellen asks what happened to the fleet. Tigh explains that every watch they update their emergency jump calculations with new star fixes to compensate for inertial drift, and then transmit them to the rest of the fleet. This time. however, Galactica's updated theirs, but neglected to transmit them to the other ships. When he mentions it was Gaeta who forgot to send the updates, Ellen is quick to attack him, but Tigh counters that it wasn't "the kid's fault".
- Ellen then tells him that now he is the one in charge of the fleet to which Tigh responds that it is not his command, no matter how much Ellen wants him to be.
- Later upon entering the CIC Tigh tells the crew in that Adama is still the commander, and will be until the day he dies, and they will not let him die. After everyone resumes their duties he turns to Gaeta and Kelly, who have come up with an idea on how to locate the rest of the fleet. If they jump back to their original coordinates, their navigation computers can use the star fixes to generate a best fit solution for the fleet's current location. However, it will take 12 hours to locate the fleet, and with a basestar in the area, they won't be able to survive long enough to jump again.
- In the brig, Apollo and Roslin talk about wanting the ship to return to their jump point, since Starbuck will have no way of locating the fleet, should she return with the Arrow of Apollo. Roslin apologizes to Apollo for making him go against his own father but he forestalls her by implying he did it for his own ideals which amounted to nothing.
- On Kobol, the survivors have made their way into the trees and Baltar sees a baby cot as they walk further in.
- The team decides to stop and Seelix looks for some more serisone. Tyrol asks Socinus how he is doing to which he replies that he can hear birds, something they have not heard for a while.
- Seelix is unable to find the second med kit which contains the needed serisone. Crashdown blames Tarn for not bringing it and orders him to retrieve it alone; however, the Chief and Cally are able to convince Crashdown that they should go with Tarn as backup. The three then head back to the Raptor crash site.
- On Caprica, in the Delphi Museum of the Colonies, Kara Thrace and Karl Agathon look over the body of the dead Six. Sharon then warns them that they need to leave, as the Six will download into another body and reveal their location to the other Cylons.
- Starbuck is annoyed that they are to listening to a Cylon though Helo counters that Sharon has gotten him this far. Sharon also tries to convince Starbuck by reciting a memory she has of her.
- Starbuck reacts by pulling out her gun and pointing it a her. Helo tries to stop her from shooting but Starbuck doesn't listen and pulls the trigger her shot missing when Helo pushes her arm and then revealing Sharon is carrying his child.
- Starbuck is upset at Helo for falling for a machine and they begin to argue until they hear a noise. They rush outside just in time to see the Raider Starbuck arrived in flying off. The scene ends with Starbuck exclaiming "bitch took my ride."
- Tigh visits the sickbay, and he has another flashback of himself and Adama in a bar during which Adama tells him that he is going back to the fleet.
- Tigh subsequently talks to Layne Ishay, who tells him that Adama has lost a lot of blood, and the bullets have damaged his spleen. She feels unequal to the task being only a medic and wants Dr Cottle to operate. Tigh informs her that he is not available and she will need to perform the role of a doctor in order to save Adama.
Tigh brutalizes Valerii during her interrogation.
- After leaving sick bay, Tigh heads to the brig where Boomer is being held to question her. He orders her to tell him how many Cylons are in the fleet and who gave the command to shoot Adama. Boomer, still in shock at what has happened is unable to answer until she finally says 'just get it over with, you frakking coward."
- Angered by her reply, Tigh beats her, and orders one of the Marines to give him a sidearm so that he can shoot but is stopped from doing so by a memory of a door with the number 3 on it that is about to be opened.
- On Kobol Tyrol, Cally and Tarn return to the Raptor crash site, find the missing medkit. and make their way back to the rest of the team.
- As they walk, Cally and the Chief engage in some light banter when they suddenly fall under gunfire.
- Cally and Tyrol are able to take cover but Tarn is shot twice in the chest before he can do the same. Tyrol gives Cally the rifle so she can cover him while he tries to get to Tarn, who is shot once more. Tyrol manages to reach him, picks him up and moves away from the firing Cylons with Cally in tow.
- Once the Chief and Cally manage to evade the Cylons, they stop to check on Tarn's Condition. Tyrol is reassuring him when he stops breathing and dies. The Chief is momentarily at a loss but finally takes Tarn's dog tags, and the two continue on.
- On Galactica Dualla and Gaeta are washing up in the officer's Head where she tries to comfort him by telling him that their current situation is not really his fault. After she leaves, Gaeta becomes inspired by the arrangement of soap bars next to the sinks to build a firewall for Galactica's computers, and rushes to the CIC to present his idea to Tigh and Kelly.
- In CIC Gaeta explains that they could calculate the fleet's location in 10 minutes if they network the ship's computers.
- Kelly objects to the idea, bringing up Commander Adama's past reluctance to networking which would make them vulnerable to a cyber-attack by the Cylons. Gaeta counters by explaining that he would devise a series of firewalls to halt the virus protecting the mainframe. Having no other good options, Tight gives his approval for Gaeta to proceed.
- As they prepare to jump to their previous location, Tigh has another flashback. In this one Adama informs him that he is back in Colonial Military due to his wife's connections with the Defense Subcommittee. Confident, Adama tells Tigh that he will command his own battlestar one day.
- Tigh decides to conditionally release Apollo so that he can resume his role as CAG, though he must return to the brig when not on duty and not attempt to free Roslin. As the Colonel is leaving the brig Roslin talks to him but he refuses to hear her.
- Back in CIC, Gaeta has networked the ship's computers and set up five firewalls to protect them. Although Gaeta is less than confident and expresses that would have liked Baltar's help, Tigh says he trusts him, and will take his work "over that shifty son of a bitch any day."
- Once everything is ready, Galactica jumps to their previous location and start the calculations. Multiple DRADIS contacts are detected: the basestar and raiders, who prepare to attach them.
- Galactica holds off the Cylon basestar with weapons fire, while the Vipers are launched to intercept the raiders. Those in the cockpit include Apollo, Kat, Flyboy and Hot Dog.
- One of the Raiders sends a computer virus to Galactica, which immediately tries to infect the computer systems and quickly breaches the first firewall.
- While engaging the Raiders, Apollo notices a strange Cylon vessel among them and engages it with Kat's assistance.
- While the ship is taking hits from missiles, Ishay and her team begin to operate on Adama. His heart stops beating and unable to use the defibrillator to restart it, Ishay asks for a surgical knife.
- In the brig, Corporal Venner asks for Roslin to pray with him.
- The second firewall is breached while the jump calculations are only halfway done, followed soon after by a breach of the third.
Apollo nears the flak field while trying to stop the Heavy Raider.
- Apollo nears the strange Cylon vessel, which turns around and tries to destroy Apollo's Viper. He manages to damage the ship, but it reverses course and heads directly towards Galactica. Kat urges Apollo to halt pursuit, since he is getting too near Galactica's guns. Eventually, Apollo has no choice but to disengage and Heavy Raider crashes into Galactica's starboard flight pod.
- Ishay opens Adama's chest and performs a heart massage.
- The fourth firewall is breached leaving only one protecting the ship's computers from being overtaken by the Cylons.
- Finally, calculations are complete and Gaeta breaks the network link.
- All Vipers are ordered back to the ship and Tigh orders a jump to the fleet's calculated location.
- After the jump, Gaeta reads DRADIS, reporting several signals which turn out to all be Colonial. The calculations were correct and fleet has been found, elating the crew. Tigh is quick to order the Rising Star to send Cottle over the Galactica ASAP.
- In sickbay, Tigh congratulates Ishay for her work to revive Adama, and stop the bleeding. After she leaves, Tigh talks to Adama who is still unconscious, and wonders if he can hear him.
- Tigh has another flashback, involving the same "3" door seen earlier. It opens with Tigh dousing his uniform and metals in lighter fuel preparing for what appears to be self-immolation. He hears a knock on the door and after some hesitation, he answers it. Two MPs, inform him that he is back in the fleet courtesy of "Major Adama".
- After the flashback, Tigh tells Adama that he shouldn't have let him back into the service, instead letting him die along with the other billions of people killed during the Cylon attack. He never wanted command, and urges Bill not to die.
- Meanwhile, in the starboard flight pod, the wreckage of Heavy Raider seems completely quiet as it rests in Galactica's museum. Suddenly the red pulsating eyes of several Cylon Centurions appear as they emerge from the damaged craft and into Galactica.
- The second season introduces the practice of showing the current Fleet population in the opening credits. Throughout this episode, that population is 47,875. That represents 12 total casualties since "Kobol's Last Gleaming, Part II".
- Socinus's lungs are filling with fluid.
- Captain Kelly is third in the chain of command, after Tigh. This is demonstrated in the Miniseries, as Kelly attempts to give orders on trying to stop the fires after the nuclear strike on the battlestar, while Tigh hesitates giving the order to vent the affected compartments.
- It is possible that Kelly is only third in command because of the "malefactions" of Apollo, and that, typically as fourth it is not a surprise that he is not seen before. The sudden incapacity of two superiors has bumped him up the ladder.
- While Doctor Cottle holds the rank of Major, as physician he would not be in Galactica's chain of command at all. In the military there are times when a lower ranking person will be in "operational command" of people who are technically higher in rank. This is the distinction between a staff officer and a line officer. Line officers are those officers in general military specialities, and are eligible to command ships and other units. Staff officers, however, are only permitted to command units within their speciality (like medical personnel). Aboard ships, the senior line officer is in command, no matter the rank of any embarked staff officer. While the line officer will treat the staff officer with all courtesy and respect of the higher rank, the line officer is not obligated to follow any orders of the staff officer not within the staff order's speciality. This is how a doctor (staff position) may remove a line officer who is not fit for duty from command, but may not assume command unless all line officers are incapacitated.
- Adama and Tigh served on a merchant freighter together after leaving the military; Adama was responsible for bringing Tigh back into the military when he reentered.
- This episode marks the first (known) attempt at networking Galactica's computer systems, at least under William Adama's command.
- Tigh's distrust of Baltar seems evident in this episode, particularly in the reply he made to Gaeta regarding the trust he had in the Lieutenant's programming abilities over Baltar's.
- Tigh's wife has taken residence in Tigh's quarters.
- Starbuck seems to incorrectly assume that there is a "real" Sharon Valerii and that the Valerii on Caprica is just a copy of her.
- This episode introduces the first combat depiction of the Cylon Heavy Raider, previously seen during "Colonial Day".
- This episode shows the first change in the intro sequence, including subtitles, a lack of the "episode clip" sequence, and the use of the theme music previously used only in the UK showings of the first season.
- Kerry Norton (paramedic Layne Ishay) is the wife of Jamie Bamber (Lee "Apollo" Adama)
Gaeta's firewall under attack, but not (yet) breached.
The virus breaches Gaeta's last firewall on the display in the upper-left corner.
- As Gaeta leans away from the status display to the floor to yank out the cable networking the computers (while he's not looking), the display does show that the last firewall is breached (probably why the Cylons were able to infiltrate a few but not all of Galactica's computers). Once he unplugs the network, the firewall status disappears from the screen. When he sits up and looks at the screen, it only says that the fleet position is plotted and that the network is offline.
- In this episode, the viewers discover that Captain Aaron Kelly is third-in-command, but haven't really seen that much of him since the Miniseries (although he is doing his job as Landing Signal Officer in "Final Cut"), which makes this seem contrived. However, in the Miniseries, Kelly gives Tyrol an order to aid the stricken port flight pod rescue after Tigh hesitates to give an order (himself following Adama's command to tend to the matter). Giving such an order with the second-in-command standing there is something only a third-in-command would have the guts or authorization to do. Tigh did countermand him moments later to order the venting of the pod, but did not suggest he was out-of-line for stepping in. This strongly suggests that Kelly already was third-in-command, either at the time of decommissioning or as a direct result of casualties taken in the attack. Additionally, "Final Cut" seems to establish that as LSO, he just spends most or all of his duty time in the flight pod, and thus wouldn't normally be seen in CIC. Given that a battlestar's initial defense involves the reliability of Viper launches, Kelly's rank and duties could be considered just as important as the command staff needed to initiate the launch orders.
- "The appearance/disappearance of Captain Kelly has more to do with the budgeting process on the show than any creative issue. We only have so much money to spend each week and it's not worth it to pay to bring in Kelly (or any other recognizable guest-star for that matter) unless he's integral to the plot. So, we ask you to take the leap with us and assume that characters like Kelly and Kat and Hotdog and so on, are still aboard ship and doing their jobs even when they're not featured on camera, and therefore are ready to step into action the moment we actually need them for a story."
- The starboard flight pod is significantly damaged in this episode. However, as Ron Moore states in the audio commentary (podcast) for this episode, that this landing pod - originally set up as a museum - is not in active use.
- Computers simply being networked is not a sufficient condition to allow foreign interference - why would any of the systems Gaeta links be connected to wireless channels? Is the infiltration that he detects originating from within Galactica?
- As with any other Colonial ship, Galactica receives data all the time from exterior sources. In addition to its mainframe computer, Galactica primary computers include the FTL, Navigation, Damage Control, and Fire Control systems. The mainframe ostensibly handles wireless communications (Note Caprica-Valerii's request for access to the mainframe with its communications channels in "Flight of the Phoenix"). The mainframe probably did come under attack by the Cylon virus but was able to avoid infection because a Colonial mainframe may have been what the Colonials believed would be the central lynchpin in stopping any Cylon computer cracking.
- While the Colonial Fleet became lax in their computer defenses years after the Cylon War, they probably believed that a networked computer system would be acceptable provided that their battlestar's mainframe computer or a robust avionics package and programming would be able to block or stop any electronic incursion. That fact might have been true -- were it not for the Command Navigation Program, which gave the Cylons a backdoor to any Colonial flight computer system. Instead of ramming the main door (mainframe) down, the Cylons used the "window", entering through a lesser computer (or opening a hole in their network) to achieve the same effect. The CNP helped to bypass the defenses of the mainframe, where normal communications were probably screened and electronic attacks thwarted, to enter through another system.
- Galactica's computers may have never been networked in her history before this episode. Her computers may also not be as robust as her sister battlestars. But her computers were designed to be networked or run separately since Gaeta was able to set up a network at all. It was very likely that the mainframe was part of Gaeta's ad hoc network since the other computers would not be able to gather any data from the mainframe's wireless communications. Once the connections were made, the other computers (all of which probably had less resistance or defenses to Cylon viruses) were likely more susceptible to infection than the mainframe as these computers could now "hear" the same things that the mainframe heard normally in its business (such as Cylon electronic attack sequences), but was far more able to thwart. The lesser computers became infected quickly. After a time, even the mainframe in whole or in part would be infected since the Cylon virus is remarkably adaptable and polymorphic, even turning later into a Logic bomb after learning and probing Galactica's hardware (in "Flight of the Phoenix").
- See also Galactica Techblog #4 by science adviser Kevin Grazier.
- The members of Galactica's crew jump to the conclusion that Lieutenant Valerii must be a Cylon, without considering the possibility that she acted in support of President Roslin, or in collusion with one of the many dissident factions within the fleet, or that she is suffering from mental illness. The suspicious nature of her recent cheek wound should make this last concern particularly plausible.
- Does Tigh recall that Gaius Baltar first tested his Cylon detector on Valerii? Or did he know in the first place? (Answer)
- Regarding the firewall status display: What is not to say that the Cylons programmed the display, or more accurately the GUI interface for it, to show a false reading on their intrusion progress? (see Analysis for a related topic)
- Just how many aboard Galactica agree with Adama's decision to jail Roslin? (Answer)
- Is LSO Captain Kelly normally third in the chain of command on Galactica, or would a CAG outrank him if on board the ship?
- We've almost completed shooting the opening of Season Two, with Michael Rymer back at the helm filming a two-parter written by David Weddle & Bradley Thompson called 'Scattered' and 'Valley of Darkness.' Things have been going well so far, with a good mood on the set and a feeling of satisfaction and pride running through the whole team at their accomplishments in year one and anticipation for year two."
- Regarding the bar room scenes (i.e. how Saul Tigh and William Adama met) that were filmed, but weren't fully utilized:
- "We were going to open this show, with just that scene, to show how the two men met. And then come into this scene we're watching now, where Tigh takes command of Galactica, and Adama's been shot, and there's all this chaos. And the episode was going to continue to sort of flashback onto their relationship. On the early days of Tigh and Adama. [...] And we shot those sequences. And edited it together, and we looked at them, but ultimately we didn't like them. We just didn't feel -- they weren't quite the show. [...] You can't really put your finger on any particular person, except maybe me, because it is my concept. [...] I don't know if I created, or had the writers of this episode, Bradley Thompson and David Weddle, I don't know if I really gave them a rich enough environment to tell that backstory. "
- On splitting the original "Scattered" into "Scattered" and "Valley of Darkness":
- "We've always struggled with the length of our scripts, the length of our episodes. If you look at it, there's only 40 minutes and change of actual program content. And our scripts tend to run, in the early drafts, in the 50s or low 50s. [...] 60 page scripts are not unheard of. An ideal page script for us, going into shooting, is usually around 46-47 pages. Sometimes we make that, sometimes we don't. [...] And I think we did on 'Scattered', I think in the final draft it was around 47-48 pages. The shows are still too huge. They're still too long. The style of storytelling -- I might have talked about this before -- just requires spending more time on character, creating moments, really, sort of, taking your time as you go through the show. [...] So we essentially divided it into two and created another action storyline for part two."
- On the scene in which Tigh is about to commit suicide:
- "The great thing here is this is- there's a definite homage quality in this to Apocalypse Now which is one of our- a brilliant film. One of our all-time favorites and we certainly wanted to pay respect to that in certain ways with this scene. But it's not the same scene. They don't put him in the shower and sober him up. It's- he just goes off and pulls himself together. Which, for our story, is more effective. There was something great about him getting ready to light his own medals on fire with the lighter fluid and I wanted to convey this idea that he might- the whole place might go up but we didn't q- we weren't able to quite convey that."
- Jamie Bamber talks about the challenge of filming the episode's opening act:
- So far this season I've been given great stuff to do, and as my character I've been very careful not to apologize for the decision he made in Kobol's Last Gleaming. It's the one thing that Lee can claim as his own act and he's not about to second guess himself. Michael Rymer [who directed Kobol's Last Gleaming and Scattered] and I got together early on and decided that would be the case. We could have taken Lee down either path. He could have felt massive guilt in the way in which his father is gunned down seconds after betraying him, and then not having the chance to put that right. It would have been easy to go back and question what he did, but I think the character is far more interesting and stronger for not doing that. Lee is standing on his own two feet and moving forward, which he has to do. 
- In issue #348 of Starlog magazine, p.33, Nicki Clyne (Cally) said:
- "Cally is supposed to provide the Chief firecover by shooting at the Cylons. I focused on doing it right, because the weapons experts showed me how to aim and fire the guns, but the director said "No, you're shooting those weapons too well. Remember, Cally hasn't fired a weapon since basic training!" But I figured, "Hey, if I can learn to shoot a gun that quickly, then Cally certainly can". That was my defense!"
- "We shot a scene where I’m in the brig, and Tigh is trying to get in my face, and I’m all, 'Just shoot me now, you pussy.' It was great." -- Grace Park, 
- In Galactica's sickbay:
- Colonel Tigh: (to Commander Adama) You never should have brought me back into the service. If you had just let me be, I'd have died back there on Caprica along with everyone else, and been happier for it. I don't want a command. I never did. Don't you dare die on me now.
- During a flashback sequence:
- Saul Tigh: So, how'd you do it? How'd you get off this frakking freighter?
- William Adama: Connections. Anne's father has a friend in the Defense Committee.
- Saul Tigh: So the new wife comes through. I wish I had in-laws with pull.
- William Adama: Give me a couple years. I'll have some pull. You watch me. I'll have my own battlestar someday.
- In Galactica's brig:
- President Laura Roslin: (to Tigh) Colonel, once we find the fleet, I'd like to have a word with you.
- Colonel Tigh: There's nothing to talk about. You went up against the old man and you lost.
- Tigh's pep talk to the CIC crew:
- Tigh: This is his command. His orders are still the word of the Gods on board this ship. Just so we're clear. This will be Adama's command until the day he dies. And we are not going to let him die. So say we all.
- On Caprica Valerii being "right":
- Starbuck: She's right, huh? Sharon the Cylon is right. Let's all just listen to Sharon the Cylon. Do whatever she says. Because that's a good idea.
- Helo: Hey, Kara, she helped me get this far.
- Starbuck: OK. I get it. I get it, Helo. You and I go way back, so I get it. All right? I remember how you felt about her, but she is not the real Sharon. That is some cheap, knock-off copy.
- After Starbuck shoots at Caprica Valerii:
- Helo: I'm not going to let you kill her. She's carrying my child.
- Starbuck: My Gods, men are so painfully stupid sometimes! How do you know that?
- Helo: I know, all right? She's not lying.
- Starbuck: They lie about everything, Helo. Their entire existence is a lie. They're not human, Helo, they're machines. You can't have a baby with a machine.
- Helo: I don't know what to tell you, OK? But I believe her. It's hard to describe, we've been together for a long time. I mean, I know what she is, but she's not like the others! Look at me, she is not.
- Lee Adama gives his word to Tigh regarding his parole:
- Adama: All right, you have my parole. When I'm on duty, I will make no attempt to free her or sow insurrection among the crew. When I'm not on duty, I'll report back to this cell.
- Tigh: (matter-of-factly) Pre-flight brief is underway in the ready room.
- Adama: Right.