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The rebel basestar is one among many others in the Cylon fleet before a civil war broke out, segregating a number of humanoid Cylon copies of models Six, Two, Eight, and later, a lone Three from the others.
When Natalie Faust, a Six, proposes that they unbox the Threes to learn of the Final Five and has the telencephalic inhibitors removed from the Centurions to get the One, Four and Five models to co-operate, other Cylon models, led by the Ones, object to the change, orchestrating an attack on basestars controlled by Natalie's faction. The attack occurs in a remote area far from a Resurrection Ship in an attempt to permanently kill its occupants (TRS: "Six of One", "The Ties That Bind").
Natalie's basestar survives but is seriously damaged, its Raider complement all but destroyed, with only a few Heavy Raiders and at least 3 Raiders remaining. The ship is later found by the Demetrius crew, captained by Kara Thrace. They repair the basestar's FTL by cannibalizing Colonial datacord and other elements from a Raptor. To effect repair, however, the ship's Hybrid was taken offline. Another problem is that the basestar will have to jump to the fleet first, making the ship vulnerable against Galactica, but is saved after the Demetrius arrive to talk Galactica out of attacking the basestar, and they form an alliance to destroy the Resurrection Hub. (TRS: "Faith", "Guess What's Coming To Dinner?")
Later, when the basestar's Hybrid was brought online, it repeatedly jumps the ship several times following the death of Natalie, quickly gaining on the Resurrection Hub. The basestar eventually finds the Hub and instigates the Battle of the Resurrection Hub (TRS: "The Hub").
Downloaded Three calls for the Final Four to join the rebels on the basestar, and only Tory Foster does so. After Three agrees to renew their alliance with the Colonials, the rebel basestar joins the Fleet on the final jump to Earth, only to find it in ruins (TRS: "Revelations"). Admiral Adama invites their Cylon allies to follow the Fleet to find a new home. Three maroons herself on Earth with the bones of her ancestors (TRS: "Sometimes a Great Notion"). Despite not initially coming over with Foster, Galen Tyrol associates with his Cylon brethren to an increasing degree (TRS: "A Disquiet Follows My Soul").
When Felix Gaeta launches a mutiny and seizes control of Galactica, President Roslin and Gaius Baltar escape to the rebel basestar. Roslin convinces the Cylons to help her stop Gaeta. Subordinating themselves to her authority, they move the ship into the middle of the Fleet so that Gaeta cannot fire upon them without inflicting collateral damage upon the human ships. At the height of the situation, the rebel baseship prepares to engage Galactica under Roslin's command. Adama retakes Galactica and radios Roslin to stand down the basestar's weapons (TRS: "Blood on the Scales").
The basestar has firmly joined the Fleet, both militarilly and in government. The rebel Cylons elected a Six named Sonja to represent them in the new Quorum which is now made up of ship's captains instead of representatives of the Twelve Colonies. The basestar's heavy raiders and their pilot Sixes and Eights are integrated into Galactica’s squadrons. As of "Islanded in a Stream of Stars", the baseship's autonomous Raiders and Centurions have not yet been similarly depicted.
When the decision to abandon Galactica is made, it is decided that the Rebel Basestar will be the Fleet's new flagship. The Cylons, through Councilman Sonja Six, welcomed Admiral Adama to transfer his flag to the rebel basestar and have already accepted his command authority. Adama directed Colonel Tigh to organize the relocation of Galactica’s military personnel and equipment to the basestar within the week.
When Adama decides to rescue Hera Agathon, the Rebel Basestar (which is by then, completely regenerated) is left behind under the command of Hoshi to protect the fleet while Galactica goes by itself to rescue Hera and battle Cavil's faction. After Galactica destroys the Colony and Cavil's faction, the basestar jumps to their location when the fleet is summoned by a dispatched Raptor.
When the Fleet discovers a habitable planet the Colonials decide to call "Earth," the rebel humanoid Cylons decide to join the humans in building a new civilization on this world. The basestar is left in the hands of the Centurions who are now free to seek out their own destiny. Although some, like President Romo Lampkin questioned the logic behind the decision, fearing potential retaliatory attacks by the Centurions on the undefended settlements of Earth, Ellen Tigh and Admiral William Adama felt that giving the Centurions their freedom would be enough to break the Cycle of violence. The Centurions depart in the rebel basestar - the only ship in the Fleet that is not abandoned and flown into the sun. The exact status of the freed Centurions and the basestar 150,000 years later is unknown. (TRS: "Daybreak, Part II")