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' main 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 Rebel Alliance with Humans

The Demetrius 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 . Against her crew's opinion Kara Thrace decides to jump to Conoy's damaged baseship (The Road Less Traveled).

Thrace ultimatly takes a Raptor to the scene of the battle between Cavil's baseships and Natalie's. She finds mostly wrekage and only Natalie's basestar is still intact albiet very severly damaged. The ship's FTL Drive is down so they hook the Basestar to Kara's Raptor's FTL drive in order to jump. The Eights of this faction decide to try to revolt and turn to Athena to lead them. Athena says no and tells them off for trying to rebel. A Six kills one of the humans as she had been drowned by her for no reason on New Caprica and was emotionaly traumatized from it. Natalie kills her in order to appease the humans and like the other Cylons who died in Cavil's attack, she can't ressurect as the Ressurection Ship is too far away and under Cavil's control. Kara goes to the Hybrid who gives her a cryptic message before an Eight attempts to disconnect her. A Centurion shoots and mortally wounds her before being killed by Kara and this Eight apologizes to Athena and asks for forgivness for her actions in trying to incite a rebelion against Natalie. Athena doesn't forgive her, but Anders holds her hand and comforts her as she dies for the final time. The rebels jump the baseship to the Demetrius getting there just as the ship is about to jump and join up with the humans. (Faith)