Cylon Civil War
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The Cylon Civil War is a conflict between two factions of humanoid Cylons. One faction consists of the Number Ones, the Number Fours, the Number Fives, and the Number Eight copy known as Sharon Valerii, under the leadership of the Number One copy known as Cavil. The opposition, known as the rebel faction, consists of the Number Twos, the Number Sixes, several Centurions with restored free will, and the majority of the Number Eights, under the leadership of the Number Six copy known as Natalie. Natalie is later slain, and leadership of the rebels is taken up by the restored Number Three copy known as D'Anna until she elects to remain behind on Earth for the rest of her days. The only real battle of the war is the Battle of the Resurrection Hub, where the Rebel Basestar goes after the Resurrection Hub, but some of Rebel Cylons aid Galactica in the Battle of The Colony. That battle is the end of both wars as Cavil's faction is destroyed by Galactica and her forces in the battle. During the war, Cavil's faction controls pretty much all of the Cylons resources including all the Resurrection Ships, the Resurrection Hub and The Colony. The Rebels are unable to resurrect due to this and have to team up with Galactica's forces just to attack and access the Resurrection Hub as all of their Raiders were destroyed at the beginning, although at least 25 Heavy Raiders survived. All that the rebel faction controlled was the Rebel Basestar and what resources they had on that. Thanks to the destruction of Cavil's faction by Galactica during the final battle, the victor in the war is the Colonials and the rebel faction.
The earliest signs that the Cylons were not in perfect harmony were seen in the occupation of New Caprica, where faced with a losing battle the different models argue over the best course of action. Later the fate of Gaius Baltar is the subject of a narrow 4 - 3 vote. Sometime afterwards, the Number Threes' religious quest causes the model to be boxed.
The immediate cause of the conflict occurs at the Battle of the Ionian Nebula, in which the Cylon Raiders break off the attack because one of them detects Samuel Anders as a humanoid Cylon. Cavil's faction votes to "reconfigure" (lobotomize) the Raiders so that they will continue the attacks on the Colonial fleet. Natalie's faction votes against this action, believing that the final five humanoid Cylons are present in the Colonial fleet (TRS: "He That Believeth In Me"). Their goal is to unite all twelve humanoid Cylon models, a plan which includes unboxing the Number Threes, so that the Three known as D'Anna can tell them what she has learned in the Temple of Five.
Sharon "Boomer" Valerii's "swing vote" gives Cavil's faction the majority they need to proceed with the Raider lobotomies. Natalie's faction does not accept this and remove the Centurions' telencephalic inhibitors, releasing their self-awareness and turning them against Cavil's faction (TRS: "Six of One").
The Cylon fleet becomes split into two. A Number One remarks that Natalie "did a little ethnic cleansing", with the factions now segregated from each other among the baseships, some under Cavil's control and others under Natalie's. Later, Natalie and two Eights meet with Cavil, who tells them that after a debate the Ones were outvoted by their compatriots, who came to the conclusion that it was wrong to box the Threes and wanted to restore unity. He informs them that the Three's core consciousness is being downloaded at the central resurrection hub, and they can go to the nearest accessible server a half a dozen jumps away to listen to what she has to say. The two factions agree to go in their own respective baseships, and at the rendezvous Cavil's baseships appear without the Resurrection Ship (apparently controlled by Cavil's faction), surround the rebels, and attack, taking out the rebels' FTL drives and proceeding to destroy their baseships. Without the Resurrection Ship, the rebels realize that Cavil intends to truly kill them (TRS: "The Ties That Bind"). Only Natalie's badly damaged baseship manages to survive the massacre although all of its Raiders are destroyed in the battle (TRS: "Faith").
Proposed Alliance with the Humans
The Demetrius, commanded by Kara Thrace on a mission to find Earth, encounters a heavily-damaged Heavy Raider with a copy of Leoben Conoy aboard, who offers an alliance between the humans and his faction of Cylon rebels . Thrace orders a jump to Conoy's damaged baseship against her crew's objections (TRS: "The Road Less Traveled"), but ultimately realizes that she can't risk the entire crew, so she takes a small team in a Raptor instead, with the understanding that if she does not return within 15 hours, Demetrius is to rendezvous with Galactica.
From within the field of detonating battle wreckage, she locates Natalie's severely-damaged baseship. The baseship's Hybrid is unable to navigate a jump, but they determine that they can hook the baseship to the Raptor's FTL computer, although this would require disconnecting the Hybrid, thus potentially killing it.
The Eights want to mutiny against Natalie and turn to Athena to lead them, but Athena refuses and chastises them for too easily changing their minds and not committing to their choices.
When making the modifications to the Raptor Jean Barolay encounters a Six whom she had drowned on New Caprica. The Six, who is emotionally traumatized by that death and is enraged by Barolay's cavalier attitude about it, kills her. An angry Samuel Anders throws her down at gunpoint, but it is Natalie who pulls the trigger, both to end the Six's torment from the memories and to satisfy any human need for justice, emphasizing that there is no resurrection for these Cylons.
Thrace is brought to the Hybrid and tries to understand her cryptic messages, but is frustrated and orders that they proceed with the jump. An Eight attempts to disconnect the Hybrid, but the Hybrid's reaction causes a Centurion to shoot and mortally wound the Eight before being shot itself. The dying Eight apologizes to Athena, asks for her forgiveness, and reaches out her, but Athena doesn't take her hand. Instead it is Anders who takes her hand and comforts the Eight as she truly dies.
The renegade Cylon baseship jumps to the Demetrius, arriving moments before she is to jump back to the Fleet (TRS: "Faith"). However, when the two ships attempt to jump back together, the Demetrius fails to jump and the baseship arrives at the Fleet alone. Admiral William Adama scrambles Galactica's Vipers, thinking the Fleet to be under attack. The situation is defused when the Demetrius finally jumps and announces that the baseship is under their control (TRS: "Guess What's Coming to Dinner?").
A Plan Takes Shape
Natalie acts as the rebels' spokesperson and is brought to Galactica to talk with Admiral Adama and President Roslin. She tells them of the Cylons' central Resurrection Hub and outlines her plan. She wants to the Colonials' help in getting there and unbox the Threes. In return, she offers them a chance to destroy the Cylons' resurrection capability and take vengeance on them. Karl Agathon proposes to move half of Galactica's Vipers onto the baseship and use it to fool the Cylons. Roslin agrees, but adds a double-cross, because she distrusts the rebels: Go along with the plan, but then keep the Final Five, once uncovered, until they reach Earth.
The Cylons plan to double-cross the Colonials as well. Suspecting that the Colonials won't allow them to have the Final Five and just leave, they plan to use the Centurions to take hostages after the mission. However, after Natalie is asked to speak in front of the Quorum of Twelve to assuage their fears about the alliance, she has a change of heart. Fearing that the Final Five may watch and judge them for their actions, she tells Number Two to call off the Centurions. She also tells the Quorum that she thinks that the Cylons need mortality to lead meaningful lives, when asked why she would give up the location of the hub (TRS: "Guess What's Coming to Dinner?").
Before the plan sets in motion, Natalie is shot by Sharon Agathon, to prevent Hera from being taken. Without warning or command, the Hybrid jumps the rebel baseship from the Fleet, ending all communication with Galactica, and taking half of her air wing and Laura Roslin with it (TRS: "Guess What's Coming to Dinner?"). Later, a recon Raptor sent by Galactica finds the Resurrection Hub destroyed, as well as debris of a baseship and a number of Vipers. This indicates that Cylons and Colonials fought together and that some of them escaped alive (TRS: "Sine Qua Non").
Attack on the Hub
The Hybrid panics after sensing Natalie's shooting and death, and as a result jumps. She then continues to make subsequent jumps, each bringing it closer to the Hub, giving the combined force a chance to implement their plan. The human pilots are initially very reluctant to fly alongside Cylon pilots, but are persuaded to trust them.
After the Hub is stranded by disabling its FTL drive, Karl Agathon and the Eight board the Hub in a Raptor, find the un-boxed Number Three, and escape with her. Meanwhile, the rebel baseship exchanges missile fire with the two escort baseships. Once Three, Agathon and Number Eight are clear of the Hub, the Vipers launch several nuclear missiles at it, destroying it and at least one the escort baseships.
Aboard the rebel baseship, Three is questioned by President Roslin but refuses to give up the identities of the Final Five until she is sure she is safe. The baseship returns to the rendezvous coordinates, where they are met by a waiting Admiral Adama in a Raptor (TRS: "The Hub").
The Standoff with the Colonials and the Discovery of Earth
The Cylons, now led by D'Anna Biers, hold the Colonials hostage in an attempt to lure the Final Four out of hiding. Foster joins them on the rebel baseship, but the other three remain on Galactica. After the Cylons kill the first hostage, President Lee Adama orders a risky rescue operation. However, when Kara Thrace finds a signal giving them a direct bearing towards Earth, Adama decides to share this information with the Cylons instead. Together they jump to Earth, but discover it to be a nuclear wasteland (TRS: "Revelations").
Both humans and Cylons are devastated by the discovery that Earth is an almost dead planet which cannot be resettled due to low-level radiation remaining in the ecosystem. Teams of Cylons digging through the ruins are surprised to uncover the remains of Centurions. Their testing methods determine that all the humanoid remains on the planet are of humanoid Cylons like themselves. The Thirteenth Tribe were Cylon, and destroyed themselves. The Colonial fleet and rebel baseship decide to leave this system and search the universe for any other possible habitable planets. D'Anna gives up on the whole cycle of life, and remains behind (TRS: "Sometimes a Great Notion").
The rebel Cylons believe that they are safer with the Colonial Fleet should Cavil's forces find them. Represented by Galen Tyrol, they propose to Admiral Adama upgrades of the Fleet's FTL drives with Cylon technology, making them at least three times more efficient, in exchange for full citizenship and representation on the Quorum of Twelve. Adama sees the necessity of the upgrades but is more reserved about the rest of the deal. Throughout the Fleet, widespread sentiment is against accepting the upgrades or allowing any Cylons onboard their ships, and a runaway tyllium refinery ship is the first sign of rebellion against the the admiral (TRS: "A Disquiet Follows My Soul").
When Felix Gaeta leads a mutiny aboard Galactica, the Cylons support Admiral Adama and President Roslin. Tyrol somehow manages to communicate with them undetected by CIC and has them send a Raptor to extract Baltar, Roslin, Colonel Saul Tigh and Admiral Adama using a forgotten secondary storage airlock. Roslin and Baltar leave, but Tigh and Adama stay behind to make sure the President's Raptor gets out safely (TRS: "The Oath").
Gaeta orders the Vipers on CAP to destroy the Raptor, and Narcho tries to take it out with a missile, but it misses and hits the baseship, causing the Cylons to think they're under attack. Aboard the baseship, Roslin defuses the situation, citing Hotdog's refusal to shoot as proof that the Fleet is not solidly behind the mutiny, and urging the Cylons to stay put and give Adama a chance to save the Final Four still in the Fleet. While Roslin attempts to broadcast to the Fleet using the Raptor's wireless, the Cylons note among themselves that the Fleet has dispersed and left them vulnerable, and Viper patrols are acting aggressively, trying to provoke a response. After discussing the situation they tell Roslin they have decided to jump away, but Roslin argues they should give Adama a chance and show that they are with him and the Fleet. With the help of a Number Two, she succeeds in penetrating Galactica's jamming long enough to make a transmission to inform the Fleet of the mutiny aboard Galactica and persuade ten ships to spin down their FTL drives. She then broadcasts orders to the mutineers to release their prisoners, return command of the Fleet to Admiral Adama, and surrender. When Tom Zarek responds as President of the Twelve Colonies and says that Admiral Adama and Colonel Tigh are dead, she has the Cylon baseship turn its weapons on Galactica. Gaeta orders Galactica and its allied ships to to jump away, not wanting anymore bloodshed, but Tyrol disables Galactica's FTL seconds before the jump is initiated. On the brink of a shooting war between the baseship and Galactica, Gaeta orders weapons hold just before the CIC is retaken by Adama and his supporters. Adama then contacts the President to inform her and the Cylons that Galactica is secured and to stand down. Gaeta and Zarek are later executed for their actions and the rest of the mutineers are jailed (TRS: "Blood on the Scales").
In fulfillment of the deal brokered by Tyrol, the Cylon rebels are granted a seat in the Quorum of ships' captains and elect a representative, a Number Six named Sonja. While meeting with Admiral Adama, President Roslin, Lee Adama, and Galen Tyrol, Sonja informs them that when the Quorum convenes, she intends to formally request they hand over Sharon Valerii, who returned to the Fleet with Final Five Cylon Ellen Tigh, so that she can tried for treason. It is unknown whether or not the Cylons have been upgrading the Colonial FTL drives as part of the deal yet or not (TRS: "Someone to Watch Over Me").
Members of the Rebels continue to help repair Galactica although one of the Six's gets into an argument with a human tech. However, she later saves his life at the cost of her own. In a comment that's made, it's confirmed that the Cylons have indeed upgraded the Fleet's FTL drives, although for some reason at least one Raptor (stolen by Boomer to escape with Hera Agathon) wasn't upgraded. The effect of these upgrades is easily seen: when Boomer's un-upgraded stolen Raptor travels to The Colony it takes over a dozen jumps, but the upgraded recon Raptor sent to check it out and later Galactica herself are able to make it in one jump. Everyone expects Galactica to have to be abandoned and the Cylon Rebels inquire about the timetable for Admiral Adama transferring his flag (i.e., relocating himself and his command staff) to the Rebel Baseship; presumably, Galactica’s entire military complement would be reassigned to the Baseship, it being the only other warship in the fleet and being capable of accomodating Raptors and Vipers. The Rebel Cylons have no problem with letting Adama take command of the baseship and are willing to follow his orders. Sixes and Eights fly their Heavy Raiders in integrated CAPs and other missions with Colonial pilots in Vipers and Raptors. Rebel Cylons have joined in the practice of posting photographs of their dead in Galactica’s Memorial Hallway.
When Hera Agathon is kidnapped, the rebels push for her rescue, but Adama is unwilling to commit the two warships at his command to a likely suicidal rescue mission, although he does agree to send a Heavy Raider on a recon mission that shows that The Colony has been moved. Galactica is stripped for parts and the crew is started to be transfered. After an encounter with Hotdog and seeing Hera's picture on the Memorial Wall, Adama decides to try a rescue mission. After learning The Colony's location from Anders, Adama decides to commit Galactica to the rescue mission, making it volunteer only. The Final Five, many of the pilots and marines, some of the deck crew, Doc Cottle (who's sent back), Ishay, Apollo, Starbuck, Baltar (ultimatly), Caprica Six, Helo, Athena and even Roslin end up volunteering along with some of the mutineers who are pardoned in exchange. A recon Raptor is dispatched and it locates The Colony in orbit of a black hole. The rebels add a force of Rebel Centurions and the Rebel Baseship is left behind to protect the fleet under the command of Hoshi while Galactica launches its rescue mission.
End of the War
The Rebel Basestar stays behind as the Fleet's new flagship with most of the Rebel Cylons while Galactica travels to The Colony to rescue Hera Agathon. The only Cylons that go are Caprica Six, the Final Five, Athena and some Centurions painted with a red stripe (presumably to distinguish them from Cavil's Centurions). During the Battle of The Colony, Hera is rescued and many of the enemy Cylons fall including Boomer (who somewhat reedems herself by helping Hera escape) and Cavil who kills himself. The Colony is knocked into the black hole it orbits and is destroyed along with presumably all other Cylons in existance. With the destruction of The Colony and Cavil's faction by Galactica, the Colonials and Rebel Cylons officaly win the war. Galactica escapes and finds a new home for the Fleet. The Twos, Sixes and Eights decide to stay with the humans on their new home planet that they decide to name Earth and give the Rebel Basestar to the Centurions to find their own destiny and freedom. They know there's a chance the Centurions might rebuild and come after them again in the future, but they believe that giving them their freedom may break the cycle of violence and prevent that. With the destruction of Cavil and his faction, the Colonials and Rebel Cylons are able to live out a peaceful existance together on the new Earth and eventually die of natural causes (presumably).
Resources the sides possessed
During the Civil War, both sides possessed differing resources. At first, both sides controled a fleet of ships and a lot of resources, but this quickly changed. Despite the rebels initaly possessing a lot of ships, Cavil controled all of the Resurrection Ships and this was crucial in his initial victory over the rebels. He was able to ambush the rebels with the Resurrection Ship gone and destroy most of them, leaving only one badly damaged basestar that somehow managed to survive the ambush. Thanks to Cavil controlling the Resurrection Ships, none of the rebels could resurrect and were rendered mortal. Cavil also controlled the Resurrection Hub, the hub of all resurrection that controled the process and was crucial to it. This prevented the rebels goal of resurrecting D'Anna to learn about the Final Five and also left him in complete control of resurrection. Cavil lost this and essentially the Resurrection Ships when the rebels and the Colonials managed to destroy it in a joint strike and accomplished the goal of bringing back D'Anna which was helped as Cavil brought her back himself and the rebels only had to retrieve her. Cavil and his forces also controlled The Colony, the planetoid-sized space station that was essentially the Cylon homeworld. Possession of this gave Cavil and his forces a heavily fortified defensible base to operate from and Cavil moved it before the civil war as if he was anticipating it so the rebels couldn't find it. This also proved to be his downfall as it was destroyed by Galactica and her forces (including some rebel Cylons) in a final battle and as it was housing all of his forces at the time, Cavil and his faction were completely destroyed with its destruction. Also, Cavil's faction controlled the lobotomized Raiders and the non-sentient Centurions.
The rebels, in contrast, controlled very little. When the war started, they controlled several baseships, but no Resurrection Ships or the Resurrection Hub or The Colony. After Cavil's ambush, all but one baseship that somehow survived were destroyed and all the rebels controlled was that baseship and all that was on it. It took several months for the baseship's damage to repair itself and by then the war was just about over and the ship participated in no more battles after the repairs were finally done. All of their Raiders were destroyed in the ambush, although at least 25 Heavy Raiders survived the battle. In order to even attack the Resurrection Hub, the rebels were forced to team up with the Colonials as they just didn't have the resources to attack by themselves. Later, the rebels decided to stay with the Colonial Fleet as they felt safer there with Galactica to help back them up. The rebels also possessed sentient Centurions.