Fall of the Twelve Colonies
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The Fall of the Twelve Colonies (also known as The Fall, the Cylon attack, Cylon holocaust or Second Cylon War) is a devastating, genocidal attack by the Cylons, designed by John Cavil to eliminate the human race, and seek revenge on the Final Five for creating the humanoid Cylons in their image.
Before the Fall
The events leading up to the attacks go back at least a few years, when the Cylons (now in human form) begin infiltrating Colonial society. One such Cylon, a Number Six, is involved with Dr. Gaius Baltar, a famed computer scientist living on Caprica. Together, they develop system upgrades for the Colonial Fleet, which gives Six access to the Colonial Defense Mainframe. There she is able to covertly install backdoors into the new software which the Cylons will later use to shut down Colonial defenses (TRS: "Miniseries").
Six years prior to the attacks, Commander William Adama, aboard the battlestar Valkyrie, is tasked by Colonial admiralty to launch a stealth plane across the Armistice Line into Cylon held space. Piloted by Daniel Novacek, the bird is discovered by an unknown contact, and is shot down by Adama to prevent his pilot from being potentially captured by Cylon forces. The plan fails, and Novachek is captured anyway after he ejects from the Stealthstar, and remains in Cylon custody for at least eight years (including two years post-fall), until he is deliberately released by the Cylons in the hopes that he will kill Adama for his actions. Adama spends the next few years feeling guilt over the incident, which has him thinking it caused the Cylon attacks (TRS: "Hero").
In the final weeks before the attacks, copies of the Cylon John Cavil visit the Colonies in order to ensure everything is set. One copy meets with the Number Six on Caprica, passing details about the Colonial computer systems from her to the Cylon fleet, while another meets Ellen Tigh at a bar on Picon minutes before the attack begins, to see if she has changed at all. This copy is visibly upset when he discovers she has not (TRS: "The Plan").
Prior to the attacks, the Cylon fleet is amassed around the Colony, the Cylons' "homeworld." When the command is given, the basestars jump to their targets before striking. It takes the Cylons all but three minutes to access the defense mainframe and shut it down, leaving the Colonies and the Colonial Fleet defenseless (TRS: "The Plan"). This infiltration of Colonial systems combined with the "complete surprise" that the Cylons achieve enables them to sweep the Colonial Fleet aside with minimal losses, a triumph beyond their most optimistic projections (TRS: "Downloaded").
The Cylons begin their attack by first jumping to the Armistice Station. The Colonial officer on duty is shaken when a vessel docks with the station and two Centurions enter the meeting room, followed by a Number Six model. The Six approaches the officer and begins to kiss him passionately. A nearby basestar opens fire at that moment, destroying the station.
The Colonial Fleet
Having received the CNP “upgrades”, the Colonial Fleet is easily shut down by attacking Cylon Raiders. The fleet loses at least 30 battlestars (Among these, Yashuman and Valkyrie) in the opening wave, which according to Kara Thrace, is a quarter of the fleet. After this news is broadcast, Admiral Nagala takes command of the battlestar Atlantia, and begins a counter attack near Virgon’s orbit, as per a system plot by Lt. Gaeta aboard the battlestar Galactica. The battle doesn’t last long, and Atlantia is lost along with the battlestars Triton, Solaria, Columbia, and others, prompting Galactica commanding officer William Adama to take command of the Fleet, and ordering remaining forces to Ragnar Anchorage for regrouping.
The battlestar Galactica, approximately 300 million miles from Caprica at the time, is largely unprepared for the attacks, having just been decommissioned and transformed into a museum. It dumps its munitions as part of the decommissioning ceremony, and has lost its primary fighter wing. However, as part of the museum, it has a handful of older Viper Mk II's aboard, which Commander Adama has put to use, as Galactica is attacked herself. Here, the attacking Raiders try to shut down Galactica and her Vipers, but since she has no networks, the shutdown command has no effect. The handful of planes are enough to hold off the attacking Raiders, however, not before a Raider fires off her nuclear tipped missiles in a last ditch attempt to destroy the battlestar. Out of three missiles fired, Galactica pilot Kara Thrace manages to shoot down two, before the last one strikes the battlestar. Galactica comes out relatively unscathed, with the ship's armor plating keeping out the hard radiation. After the blast clears, the ship's port stern thrusters get stuck on, pushing the battlestar into an uncontrollable lateral counterclockwise spin. The port flight pod suffers the most damage, with violent decompressions along the forward sections. 85 crew members are lost when damage to the fire suppression system necessitates the venting of the pod's atmosphere to prevent the fuel lines from igniting, thus preventing the destruction of the ship. From here, Adama takes command of the fleet, and orders the ship to prepare for an FTL jump to Ragnar to re-arm (TRS: "Miniseries").
The battlestar Pegasus, under the command of Rear Admiral Helena Cain, is docked at the Scorpion Fleet Shipyards at the onset of the attacks undergoing a system refit, which left its computer networks offline. Most of the crew is about to take shore leave when the Cylons strike the shipyards. The battlestar is heavily damaged in the opening salvo and there are many casualties, however, thanks to DRADIS interference, the Cylons were not able to confirm its destruction, and continued their assault on the other battlestars and support ships docked at the yards. Not wanting to give the Cylons time to realize their mistake, Cain orders a blind jump away from the combat zone. The ship re-emerges several plotted jumps away from the Colonies. After sending a recon Raptor back to the colonies to confirm their destruction, the crew begins to make repairs, while Cain plots her next move (TRS: "Pegasus", "Razor").
With these Colonies (and presumably all the others) struck, the Colonials are defeated. After losing the Fleet Headquarters, President Richard Adar offers the Cylons a complete and unconditional surrender. However, the gesture is ignored by the Cylons, and they continue their assault. Adar and his administration are presumed killed a short time later, and Secretary of Education Laura Roslin is sworn in as successor aboard Colonial Heavy 798 after Case Orange is broadcasted.
Civilians Under Attack
At the onset of the attacks, there were many civilian transports and passenger liners in the space lanes near Caprica. After the Colonial Government shut down these lanes, these ships became trapped and were attacked as they were found by the Cylons. It's not long before Roslin takes the effort to round up the survivors and form a caravan to help get the civilians out of harms way, and sends out Sharon Valerii in search of more ships. Valerii is able to recover at least three homeless Vipers, and numerous transports, her last being a tylium transport, before the Cylons jump in and scan their caravan. At this point, Roslin makes the decision to abandon the sublight only ships, and orders the remaining FTL capable ships to jump to Ragnar to rendezvous with Galactica. Among chaotic comm chatter, prayers, and spite, the fleet jumps away just as a Raider Squadron jumps in. Around 20+ sublight ships, including a Botanical Cruiser are left behind, and destroyed (TRS: "Miniseries").
An additional small caravan of civilian ships, led by the transport Scylla, are able to survive on their own for a few weeks after the attacks. The Cylons are the first to find them, and attack. The Scylla and a handful of others are able to escape the attack, and survive on their own until being found by the wandering Pegasus. The civilians are thrilled to see friendly forces, however, their joy is short lived. After taking the fleet by force, Admiral Cain strips the ships of crucial parts (including FTL drives), abducts many of the civilians for service aboard Pegasus, and leaves the rest to their fates (TRS: "Razor").
Rendezvous at Ragnar
Galactica successfully completes its jump to Ragnar, despite not having made an FTL jump in over 20 years. the Galactica's crew immediately sets out to re-arm the ship, not wasting time. However, the specialists run into a sickly looking man pointing a rifle at them. As the CO is questioning him, a fallen charge detonates, trapping the two behind a now fused hatch. As the two seek an alternate route back to the ship, Adama's First War experiences, and the man's remarks reveal his true nature: he is a Cylon. The radiation surrounding the station has affected his silica pathways which leave him dying a slow and permanent death, however, Adama soon finishes the job after the Cylon, Leoben, is able to throw Adama to the ground. Conoy's body is transferred to the Galactica for further study.
Meanwhile, the civilian fleet arrives in orbit of Ragnar, giving the crew of Galactica a slight scare as they move down through the cloud layers. President Roslin comes aboard and asks for Galactica's protection, a notion Adama later strikes down, still hoping and preferring to take the battlestar into combat, until he realizes the Cylons followed them to Ragnar, and are now waiting for them to re-emerge from the gas giant. After deliberating with the President and his executive officer, Saul Tigh, Adama orders the fleet to prep for a jump to the Prolmar Sector, far beyond the Red Line, where he hopes the civilians will be safe.
Galactica is able to emerge from the cover of Ragnar's atmosphere long enough to calculate a jump, and defend the fleet as they jump away. Just as the Cylons are sending in a new wave of Raiders, the battlestar recovers its birds, and jumps to join the fleet (TRS: "Miniseries").
While Galactica and its fleet are momentarily able to escape the Anchorage, they are hounded by the Cylons, who jump to the fleet's location every thirty-three minutes. This incurs a cat and mouse game that lasts for days after the fall, until the passenger vessel being tracked by the Cylons is destroyed (TRS: "33").
The Cylons occupy the Colonies for up to nine months after the attacks. During that time, they start removing the bodies of the dead, and attempt to capture healthy females for experimentation in farms. Other models choose to replant cities and live life much as the Colonials did before the attacks. During the occupation, a few surviving Colonials wage a resistance movement on Caprica, led by Samuel Anders of the Caprica Buccaneers and unknowingly one of the Final Five Cylons. The Cylon experiment fails, and they abandon the Colonies. The surviving members of the resistance are evacuated to Galactica shortly afterward (TRS: "The Plan", "Resistance", "The Farm", "Downloaded", "Lay Down Your Burdens, Part II").
Overall, the attack is a success and a failure at the same time; as a Cavil later remarked, the Cylons "had their foot on the throat of humanity" but "failed to step down hard enough." None of the Final Five are killed, and are all reunited in the Fleet. One particular Cavil comes to look upon the attacks as a mistake. Four years later, the surviving Colonials launch an assault that seals the fate of the Cylon race, settle a newly discovered planet, and eventually abandon the last vestiges of Colonial civilization (TRS: "Daybreak, Part II").