Cylon Civil War

The Cylon Civil War is an internal conflict between 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 consists of the Number Twos, the Number Sixes, 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. 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 from the Eye of Jupiter in the Temple of Five.

Open Hostilities

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. ("He That Believeth In Me")

The Cylon fleet is split down the middle, with some basestars under Cavil's control, others under Natalie's. Wether 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. Critially, Cavil's faction has control of the 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 are really dead ("The Ties That Bind").