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

Natalie has the Centurions' inhibitors removed so that they can open fire on the models that had the Raiders' free will removed, thus starting the conflict.

Later, Natalie and an Eight meet with Cavil who tells them that their fellow Twos 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 the Cylons' main resurrection hub. The two factions agree to fly there with their own baseships respectively, 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 ("He That Believeth In Me" through "The Ties That Bind").