Cylon Civil War

The Cylon Civil War is an internal conflict between humanoid Cylons.

The initial engagement.

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 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.

The seeds for the conflict are sown during 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 (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.

First Blood

The Centurions rise up against their masters.

Cavil's faction takes the "swing vote" of Sharon Valerii as sufficient for them to proceed with the Raider lobotomy. Natalie's faction does not accept this turn of events and has the Centurions' telencephalic inhibitors removed so that they can open fire on Cavil's faction, thus starting the conflict (Six of One).

The Cylon fleet is split down the middle, with some basestars under Cavil's control, others under Natalie's. Whether this division is managed with or without bloodshed on the other basestars is unknown, but a Number One remarks that Natalie "did a little ethnic cleansing" on the ship where the first shooting happened. Critically, Cavil's faction has control of a Resurrection Ship.

Later, Natalie and two Eights meet with Cavil, who tells them that his fellows came to the conclusion that it was wrong to box the Threes, agreeing to undo their actions. Due to the massive logistical task of resurrecting that many copies, the process needs to be carried out from the Cylons' central Resurrection Hub. The two factions agree to fly there with their own respective baseships, in order to hear what D'Anna has to say. However, en route Cavil and Boomer double-cross Natalie and open fire on her fleet, destroying many of her vessels. The Resurrection Ship was prevented from jumping with them, meaning that the Cylons killed in this battle will die permanently (The Ties That Bind).

Proposed Alliance with 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 (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 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.

The newly-formed alliance nearly fractures.

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 basestar jumps to the Demetrius, arriving moments before she jumps back to the Fleet (Faith). However, when the two ships attempt to jump back together, their jump drives aren't properly synchronized and the basestar arrived at its destination alone. Admiral Adama scrambles Galactica's Vipers, thinking the Fleet to be under attack. The situation is defused when the Demetrius arrives and announces that the basestar is under their control (Guess What's Coming to Dinner?).

A Plan takes Shape

The Colonials and rebel Cylons unify under official terms.

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 (Guess What's Coming to Dinner?).

Without warning or command the Hybrid jumps the rebel basestar from the Fleet, ending all communication with Galactica. There were many Colonials aboard including Roslin, Baltar and several pilots, along with a number of Vipers and Raptors. It is as yet unknown whether the humans and Cylons aboard continued co-operating wherever they jumped to (Sine Qua Non).