Battle of Kobol (TRS)
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During a reconnaissance flight, Sharon "Boomer" Valerii and Alex "Crashdown" Quartararo return to Galactica with information on an unusual habitable planet. Though Quartararo originally proposes this planet to be the sought-after Earth, a strangely attentive Valerii explains that this is something "much more important". Investigation of the ruins and features of the planet confirm that Galactica has accidentally discovered the original human homeworld of Kobol, detailed extensively in the scriptures of the Lords of Kobol. Commander Adama directs three Raptors to conduct a thorough surface survey of the planet, particularly to note whether the Fleet could settle there.
When the Raptors jump into Kobol’s orbit, they come into contact with a squadron of Raiders. One Raptor is destroyed when it collides with a Raider, and a second jumps away to safety. The third Raptor is shot down and crash-lands in a marsh on the planet’s surface, proximal to a ruined Opera House.
Since the orbiting basestar prohibits a rescue of the surviving crashed Raptor crew, Kara Thrace suggests the use of the captured Raider (TRS: "You Can't Go Home Again") to sneak into the basestar with a nuclear warhead. The warhead would be activated shortly after the Raider’s departure, destroying the basestar and as many enemy fighters as possible. Naturally, Thrace volunteers to complete the mission.
Adama agrees to the plan, but intervention by President Roslin leads Thrace to disobey orders and to divert the Raider to Caprica in search of the Arrow of Apollo. While on a test flight—with Lee Adama as her wingman—Thrace activates the Raider’s FTL drive and jumps back to Colonial space, abandoning Galactica and leaving her crew without means by which to infiltrate the enemy basestar. This development infuriates Commander Adama and forces him to use alternative means of getting the warhead onto the enemy capital ship. Consequently, he orders a Raptor to be equipped with a Cylon transponder (to fool the Cylons into thinking that the Raptor is a captured vessel) and directs Valerii, with Margaret "Racetrack" Edmondson as her ECO, to fly into the basestar to deploy the warhead (TRS: "Kobol's Last Gleaming, Part I").
When Valerii and Edmondson arrive in orbit of Kobol, the transponder proves to function as intended, and the Raptor enters the basestar without Cylon resistance. However, once inside a problem with weapon deployment forces them to land within a habitable area and manually release the weapon. While working to disconnect the warhead from the couplings that bind it to the Raptor, Valerii encounters several Cylon copies of herself. The copies attempt to talk, and repeatedly profess their love to her, but the frightened Valerii—having successfully decoupled the warhead—flees to the Raptor and instigates a hasty departure, much to Edmondson's bewilderment. The copies detect the nuclear warhead and approach it, but nevertheless allow the device to detonate, engulfing them and their vessel.
Upon their return to Galactica, both Valerii and Edmondson are summoned to the CIC for commendation. As Adama approaches Valerii in congratulation, she retrieves her side-arm and shoots him twice at point-blank range—her latent Cylon programming having been further activated during her time aboard the basestar (TRS: "Kobol's Last Gleaming, Part II").
Scattering of the Fleet
In the chaos caused by the shooting, another basestar suddenly appears, and Colonel Tigh assumes charge of Galactica with Captain Kelly serving as his second in command. Caught by surprise and facing certain destruction, Tigh orders the Fleet to jump to emergency coordinates (pre-planned in standard procedure by Lieutenant Gaeta).
While relaying the emergency jump order to the civilian ships, Gaeta neglects to update their jump coordinates, and the Fleet departs with data not fitting the local space-time conditions. Thus, after escaping the Cylons, Galactica finds herself removed from the rest of the Fleet, which has ended up in a separate and unknown location. Meanwhile, the available medical staff attends to the near-fatally wounded Adama (Dr. Cottle is overseeing patients on another ship), and Marines drag a confused and hysterical Valerii to the brig on Tigh’s orders.
To determine the co-ordinates of the Fleet, Gaeta devises a dangerous but necessary plan. He networks the FTL computer to the Navigation, Damage Control, and Fire Control computers aboard Galactica, so that it will only take 10 minutes (as opposed to 12 hours if said computers are not linked) to compute the Fleet's location. However, not only will this involve jumping back to their previous location, where they will most certainly be ambushed by an awaiting basetsar, but networking the computers will make Galactica susceptible to Cylon infiltration. Knowing that the Cylons will attempt to penetrate any network they set up, Gaeta erects four software firewalls to slow the progress of the anticipated electronic attack.
Meanwhile, on Kobol, the downed Raptor crew - lead by an inexperienced Crashdown - attends as best they can to their injured. Socinus is in especially critical condition, having suffered severe lung damage from smoke inhalation. However, they are soon attacked by Cylons and flee in to the woods for cover.
Back on Galactica, final preparations are made to effectively deal with the imminent battle, and the battlestar jumps to her previous location where, sure enough, she is attacked by the lurking basestar. As Gaeta works to calculate the Fleet’s end-point coordinates, the basestar deploys hundreds of Raiders against Galactica and Vipers are scrambled in defense of the vessel. With Apollo as squadron leader, the air wing engages the oncoming wave of Raiders and a chaotic skirmish erupts. During the course of the ensuing battle, a Heavy Raider carrying a Centurion boarding party advances in Galactica's direction, but Apollo spots the craft and assails it with a team of other Viper pilots. After briefly trading fire with the Vipers, the Heavy Raider veers into Galactica's firing solution and crash-lands into the converted starboard flight pod, depressurizing it.
Gaeta successfully obtains the Fleet's coordinates and disconnects the network, but not before a Cylon virus infects one of the networked systems unknown to the command staff. With the crew having completed what they set out to do, Tigh orders all Vipers to retreat and the battlestar jumps away once more (TRS: "Scattered").
After successfully reuniting with the Fleet, Galactica's power systems shut down unexpectedly. Jammer reports to Apollo that the phones are working but are being jammed with unfamiliar communications – as such, they cannot contact damage control.
While crews attempt to orient themselves in the darkened battlestar and commence work to re-power the ship, the crashed Heavy Raider in Galactica's starboard landing pod deploys 10 heavily-armored Centurions. As the Cylons make their way into the ship, Gaeta notes that a virus has infected some of the ship's computers while they were networked, and that this is the likely cause of the power outage. He quickly assembles teams to clean out the infection.
When Apollo, Kat, Hot Dog and Flyboy are viciously attacked by a marauding Centurion, Flyboy is killed. After learning that the ship was boarded, Tigh orders teams of Marines assembled to deal with the Cylon menace. Having previous experience with this type of attack, he instructs the teams not to defend the gun magazines, but to try to keep the Centurions from reaching Auxiliary Fire Control and Aft Damage Control. Should the Centurions reach said areas, they will neutralize the crew by venting the ship's atmosphere, and then turn Galactica's guns on the unarmed Fleet.
Marine forces engage the Centurions throughout the ship and a team led by Lee Adama, consisting, among others, of Collishaw and Twinam, successfully destroys the last Centurions before they reach Aft Damage Control, though not without losses. Meanwhile, Gaeta and his team complete the task of cleaning out the virus, and are able to restore power and communications. They are successful for the time being, but the virus leaves behind a logic bomb (TRS: "Scattered").
Raptor Team Rescue
On Kobol - shortly after Socinus is euthanized due to his mortal injuries and Tarn is cut down by enemy fire - Crashdown and the Raptor team locate a group of three Centurions, and notice them cannibalizing a downed Heavy Raider. After some additional recon, they conclude that the automatons are using the vessel’s parts to build an anti-aircraft battery by which to destroy any search-and-rescue craft sent to find the stranded team. The battery is linked to a DRADIS dish set up some distance from the battery that is used to track incoming Raptors. Meanwhile on Galactica, Apollo begins preparations to rescue the downed Raptor crew from Kobol, and leads a team with two Raptors as part of the rescue team.
Crashdown develops a foolhardy plan to attack the command and control console at the launcher by flanking the Centurions and sending Cally on a possibly suicidal diversionary feint. As the team prepares their attack, they discover there are five Centurions, not three as initially counted by Baltar. Chief Tyrol points out that the two Centurions that guarded the dish had moved to the launcher, leaving the DRADIS dish completely unguarded. If the team can cover the one kilometer distance to the dish quick enough to destroy it, Tyrol reasons, they can render the launcher tactically worthless. Additionally, if they take this course of action, the team would not have to face the Cylons head on.
As the team detect the sonic booms caused by Raptors entering the atmosphere - indicating the arrival of their rescuers - Crashdown panics and negates Tyrol's new plan. He orders Cally to initiate the diversion, but she freezes in terror. When Crashdown threatens to kill her for disobeying a direct order, Baltar shoots him in the back, killing him. The gunshot alerts the Centurions to the team's presence and they open fire on their position.
With the Cylons quickly nearly on top of them, Tyrol hastily orders everyone flee for the DRADIS dish and the team fights a running battle with the Centurions to see who can get to there first. During the chase, Seelix is shot in the leg by an approaching Centurion, and is dragged to safety by Cally. Concurrently, the Cylon battery fires on the incoming Raptors, but Chief Tyrol successfully destroys the DRADIS dish, breaking the missiles' lock on the Raptors.
As the ground team is pinned down and nearly defeated, Tyrol makes a last stand by openly attacking the Centurions with only his pistol. Unexpectedly for him, the Centurions are obliterated by a missile fired from Apollo's Raptor. Subsequently, the Raptors land in a clearing and the survivors are returned to Galactica (TRS: "Fragged").