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Natalie Faust is a Number Six copy who leads a rebel faction advocating the search for the Final Five Cylons, believing that they have answers about the Cylons' origins and their place in the universe.
After the Raiders abort the Battle of the Ionian Nebula, Faust, a Number Two and a Number Eight approach John Cavil with the suggestion, that the Final Five are with the humans in the refugee fleet. This is fully declined by Cavil. He suggests that only the Raiders are a problem, because they extended their original programming and now violate their orders to fight the refugee fleet.
The faction led by Faust loses a majority vote to prevent dumbing down the Raiders by removing some of their free will through a surgical procedure. Faust is further dismayed that Sharon "Boomer" Valerii voted against her model to side with Cavil, thus further endangering the tenuous balance of the Cylon decision making process.
After a last attempt to stop the Raiders' lobotomization, she orders two Centurions into the conference room and reports to the attendant Number One, Number Four and Number Five copies that her faction removed the telencephalic inhibitors, which prevent the Centurions from using their higher cognitive functions. The Centurions open fire and kill everyone supporting Number One (Six of One).
Faust and two Number Eights meet with the resurrected Cavil to discuss the terms of ending the conflict. Cavil agrees to stop lobotomizing Raiders and to air Faust's proposal to unbox the Number Three line before his compatriots. Later, Cavil informs Faust's faction that their terms have been agreed to, and the fleet will jump to the nearest server to learn what the resurrected Threes know about the Final Five. This turns out to be a trap. The Resurrection Ship does not jump to the rendezvous point, and Cavil's baseships open fire on Faust's fleet, inflicting heavy damage (The Ties That Bind), with Faust's basestar being the only surviving ship from this engagement, however the ship's FTL drive is damaged beyond repair ("The Road Less Traveled", "Faith").
When Conoy returns with Kara Thrace, Sharon Agathon, Samuel Anders and Jean Barolay, faust is reluctant to take Thrace to the Hybrid, but ultimately agrees as they need the Colonials' help. When a Six—who had been drowned by Barolay on New Caprica and suffered resulting emotional trauma, despite aid from Faust after the Six's resurrection—kills Barolay, Faust kills the Six to appease the Colonials need for "justice," thus defusing a potentially explosive situation; the Six herself cannot resurrect, as the Resurrection Ship is still out of range.
Later, Faust overhears the Hybrid's message to Thrace and she is further convinced that the Threes must be unboxed, for the Hybrid claims that she alone knows the faces of the Final Five. After helping comfort a mortally wounded Eight, she leaves the Hybrid chamber to execute the jump, thus allowing her basestar to meet up with the Demetrius (Faith).
Upon returning to the Fleet with the Demetrius, she speaks with Admiral Adama and President Roslin to explain the events and goals of the Cylon rebellion and to garner support by the Colonials to find the Final Five. She also reveals information about the Cylon Resurrection Hub and its significance, as well as the reason for the withdrawal at the Ionian nebula. Afterward, she returns to the her basestar and expresses her fear that the humans will not allow them to have the Final Five and go their own way to a Two and an Eight and proposes that they take hostage as insurance after destroying the hub.
After speaking to the Quorum of Twelve to assuage their fears about the alliance, she reflects on her experience on Colonial One and feels remorse for their deception to the humans, compelled to tell the humans the truth to rectify the situation. The other Cylons protest and send her to speak with Adama to stall for time as the Two works to stop the Centurions from taking hostages as planned. When she arrives on Galactica, she encounters Hera Agathon in a corridor. Sharon Agathon, distressed over the visions she has been having and Hera's recent obsession with the Sixes, shoots Faust out of fear that she will take her child away (Guess What's Coming to Dinner?).
She is taken to Galactica's infirmary where Doctor Sherman Cottle tries to save her life. During that time, she has a vision of a sunny forest. However, she succumbs to her wounds and dies with Cottle holding her hand. Her last sight is of Cottle's masked face fading into white. With no Resurrection Ship nearby, her death is permanent (Sine Qua Non).