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The rebel basestar is one among many others in the Cylon fleet before the outbreak of the Cylon Civil War. It was captured by a Six named Natalie Faust, after she removed the Telencephalic inhibitors from the Centurions stationed aboard the vessel, where they then killed the Ones, Fours, and Fives after learning of their plan to lobotomize the Raider compliment, segregating a number of Sixes, Twos, Eights, and later, a lone Three from the others (TRS: "Six of One").
The ship is the only surviving rebel basestar out of several that breaks away from the John Cavil's Cylon loyalists. The rest of the rebel fleet is ambushed by the Ones, Fours, and Fives far from a Resurrection Ship, making their destruction permanent (TRS: "The Ties That Bind").
The Rebel Baseship barely escapes Cavil's ambush, taking refuge in the relative safety of a nearby gas giant (TRS: "Faith"). It falls under Colonial command when the rebel Cylons agree to Admiral William Adama's authority, and is directed to rendezvous with the Fleet after being located by the civilian vessel Demetrius, however, a failure in Demetrius' FTL engine causes the baseship to jump to the fleet alone, nearly colliding with several fleet vessels, and forcing Galactica to scramble its Vipers amongst the panicking civilian fleet (TRS: "Guess What's Coming to Dinner?").
Resurrection Hub and Finding Earth
Shortly after, the baseship participates in an attack on the main Cylon Resurrection Hub, jumping to it after the ship's Hybrid is brought back online. It is successful in rescuing a Three before destroying the station (TRS: "Sine Qua Non", "The Hub"). The baseship joins the Fleet as they make the jump to Earth shortly after the battle (TRS: "Revelations").
Joining Galactica's Fleet
Since joining the fleet, the ship is under constant repair, by utilizing the organic resin to restrengthen the hull, as well as rebuild the missing outer edges of the ship (TRS: "Deadlock"). Once becoming an established fleet ship with representation, the basestar is essential in resupplying the Fleet with needed supplies and equipment. In order to find a habitable planet as quickly as possible, all fleet ships were to get Cylon enhancements to their jump drives, an order which nearly caused the collapse of the already fragile population. In order to preserve their independence, the Colonials decide that no Cylon will step aboard a civilian vessel without the express permission of its captain (TRS: "The Oath").
Mutiny aboard Galactica
During the events of Gaeta's Mutiny, President Roslin takes refuge aboard the basestar after fleeing Galactica. The baseship in turn is ready to flee out of concern for its safety, however, Roslin persuades the Cylons to position themselves in the civilian fleet to prevent being fired upon. President Roslin is about to take the basestar and attack Galactica, however, the mutineers are put down before a shot is fired from either vessel (TRS: "The Oath", "Blood on the Scales").
Months after fleeing the burnt out remains of the Thirteenth Colony, the basestar is chosen as the new flagship after the order is given to abandon the crippled Galactica. Acting Admiral Louis Hoshi is given command of the baseship (and the Fleet) after Galactica leaves for the Cylon Colony, in one last draw for the child, Hera Agathon, while the baseship stays behind and maintains a watchful eye over the civilian fleet. When a habitable planet is found by Galactica, the Colonials return ownership of the baseship back to the Cylons, who in turn, give the ship to the freed Centurions remaining on board. While the Colonials settle their new home, the baseship jumps away for parts unknown (TRS: "Daybreak, Part II").