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 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).

Thrace ultimately 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 in 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 damaged from the battle and unable to navigate a jump, but determine that they can hook the baseship to the Raptor's FTL computer. The Eights want to mutiny and turn to Athena to lead them, but Athena refuses and chastises them for too easily changing their minds and not commiting to their choices.

A Six kills Jean Barolay as she had been drowned by her on New Caprica and was emotionally traumatized by it, but is killed by Natalie in an attempt to appease the humans. Like the other Cylons who died in Cavil's attack, the dead Six can't resurrect as the Resurrection Ship is too far away and under Cavil's control. Thrace goes to the Hybrid, who gives her a cryptic message, before an Eight attempts to disconnect the Hybrid. A Centurion shoots and mortally wounds the Eight before being killed by Thrace, and this Eight apologizes to Athena and asks for forgiveness for her actions in trying to incite a rebellion against Natalie. Athena doesn't take her hand, but Anders holds her hand and comforts her as she dies for the final time. The renegade Cylon baseship jumps to the Demetrius, getting there just as the ship is about to jump and join up with the refugee fleet (Faith).