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Preparation and the Attack
For two years, Caprica-Six lived on Caprica. Seducing the ambitious, self-obsessed, arrogant Gaius Baltar, she fools him into believing she was a corporate spy, seeking to gain advantage over her competitors in order to secure a lucrative defense contract. Over the course of two years, she used Baltar to gain access to his work -- even to the extent of re-writing many of his own algorithms -- in order to subvert his own Command Navigation Program for use in the forthcoming Cylon attack to cripple Colonial forces with no warning.
Near the end of the two years, she sees a baby in a pram in a market place. The baby's mother is also present but then becomes distracted with someone else talking to her. Caprica-Six takes a closer look at the baby and snaps its neck and walks away looking distressed, possibly to spare it from the imminent cataclysm. She also meets with a Cavil who she gives her a briefcase (presumably the one that contained the Cylon device seen in the Miniseries). The Cavil suggests she kill the body she's in and get a new one to prevent having to die in the attack, suggesting poison (The Plan).
As the Cylon attack begins throughout the Colonies, Caprica-Six tells Baltar how she is a Cylon, and her actual objectives for the CNP. When a shockwave from one of the nuclear bombs rips through Baltar's house, she tells Baltar to get down and shields him. Thanks to her sacrifice, Baltar survives while Caprica-Six dies (Miniseries).
It's revealed that she approached him asking for his help in conducting the corporate espionage she claimed she was conducting, but they got interrupted when Baltar gets a call about his father, Julius who he doesn't seem to care much for. Caprica Six follows him into the house and seems genuinely concerned for Julius but is sent away. Later she comes to Baltar's house and reveals that she found a nice care facility for Julius and had him moved there where he's actually happy. This seems to touch Baltar and as a result he later agrees to help her with her actions but says he's doing it for her not her company.
Resurrection after the attack
Caprica-Six is reborn into a new body and is hailed as a "Hero of the Cylon", with an unexpected side-effect. As Gaius Baltar experiences mysterious visions of Caprica-Six, Caprica-Six has received persistent visions of Baltar. When she asks the other Cylons, particularly Number Three, if Baltar was still alive, the copy of Number Three believes that he died along with nearly everyone else still in the Colonies.
Living on Cylon-occupied Caprica, Caprica-Six's visions of Baltar and her own developing feelings and intuition leads her to question some of the basic ideals that the Cylons hold dear. Unbeknownst to her, Number Three becomes distressed with her lingering attachment to Baltar and seeks to manipulate her feelings in order to make her unstable, thus giving the Cylons an excuse to "box" her. Three leads Caprica-Six to the aid of a Number Eight who was having trouble adjusting to life as a Cylon and still clinging to her old false human identity; Lt. Sharon "Boomer" Valerii, formerly of the battlestar Galactica.
Through her counseling work with "Boomer"-Eight, Caprica-Six learns that Three has deceived her; Baltar is not only alive but is also Vice President of the refugee Twelve Colonies in the surviving human fleet. After uncovering the lie about Baltar's death, she and Boomer-Eight begin to question themselves more about their brethren. If murder was a sin in the eyes of God when committed by humans, why is genocide condoned by God when committed by Cylons? Questions like these begin to take hold in Caprica-Six's mind and are compounded by feelings of guilt for her role in the attack on the Colonies.
While trapped in a garage with Boomer-Eight, Three and Anders, Caprica-Six directly confronts the hypocrisy of the Cylons and ultimately rejects the false "truths" of her existence. She chooses instead to use her newfound celebrity to speak out against the Cylon's continuing war against humanity. Together with Boomer-Eight, she sets out to bring fundamental changes to Cylon society, their first action being to save the life of Anders (Downloaded).
The attempt at benevolent dictatorship
Just over a year after the human colonization of New Caprica, Caprica-Six is one of the leaders (with Boomer-Eight and a copy of Number Five) of the Cylon forces that meets now-President Baltar. In just a few words, Caprica-Six reveals to Baltar that she remembers precisely who he is, and how she missed him (Lay Down Your Burdens, Part II).
Caprica and Baltar attempt to renew their relationship during the Cylon occupation of New Caprica, to the ridicule of some of the Cylons and the challenge of Number Three. The relationship is rocky, as Baltar's very survival rests on Caprica's feelings for him. Caprica is also the only Cylon who attempts to befriend Baltar's aides, such as Felix Gaeta. Her attempts are ultimately unsuccessful, as Baltar can't connect emotionally to her and even fails physically. Caprica is killed by a Five for protesting their treatment of Baltar, but downloads into a new body without any problems from the other Cylons such as a boxing (Occupation, Precipice).
Now spaceborne again after the failure of New Caprica, Caprica-Six appears to regret her decisions, as Baltar's status with the Cylons rests on the vote of the Sixes (Collaborators). Eventually she votes to keep him alive, though she treats him poorly up until the time he is tortured by Number Three. From then on she is sleeping with both Baltar and the Number Three that tortured him (A Measure of Salvation).
As their relationship continues and time passes, Caprica-Six begins to become isolated from Baltar and Three, who are occupied investigating the mystery of the Final Five. Eventually she confronts them on the fact. As Baltar denies involvement, Three tells Caprica that their ménage à trois is over, and that their destiny is separate from hers ("We love you too. But this is something you cannot share with us."). As Three and Baltar depart to the Algae planet, Caprica-Six is left heartbroken (The Eye of Jupiter).
In the hands of the enemy
When Sharon Agathon is killed by Helo in order to download to the Resurrection Ship, Caprica-Six is there to greet her and takes her to her child. When Boomer threatens to kill the ailing Hera, who Agathon insists must be seen by a human doctor because the Cylons are mystified by her illness, Caprica snaps Boomer's neck to prevent others from being alerted. Caprica-Six helps Agathon and child escape to Galactica. But on her arrival on Galactica, Caprica-Six is thrown in the brig by Colonel Tigh (Rapture).
(After her departure from the Cylon fleet, Caprica-Six's position of leadership is assumed by another Six copy known as Natalie.)
Following the failed interrogations of the jailed Gaius Baltar, Caprica-Six is visited by President Laura Roslin. Roslin assures Caprica that she will not be thrown out of an airlock, to which she responds with doubt, as Leoben was executed after being promised he would not be harmed. Caprica makes a deal with Roslin: give Baltar a trial, and Caprica will tell the Fleet everything she knows. Roslin likely now suspects that Caprica may be the "blond-haired" woman she saw with Baltar before the attacks due to Baltar mentioning the name "Caprica" during the interrogation, and Six telling Roslin that she is known as "Caprica" (Taking a Break From All Your Worries, bonus scene).
During Baltar's trial, Caprica begins experiencing shared hallucinations with Laura Roslin, Sharon Agathon, and Hera. The hallucinations all take place in the Opera House on Kobol. Roslin, Agathon, and Caprica-Six are searching the lobby of the Opera House for Hera. Caprica finds her, grabs her, and disappears into the main chamber of the Opera House with Baltar (although this should be her Virtual Baltar as the real Baltar is never seen waking from the hallucinations). The door closes behind them and ends the initial dream. The hallucination later continues with her and Baltar walking onto the stage of the opera house with Hera. The two of them turn around and see the Final Five standing on the balcony. They are displayed as indistinguishable white figures ("Crossroads, Part I", "Crossroads, Part II").
Roslin later visits her for information on the Final Five and Caprica Six admits she's not allowed to even think about them (which Roslin points out she is doing right at that moment) and that all she can tell Roslin is that she can sense them close by in the Colonial Fleet (He That Believeth In Me).
When Colonel Tigh visits Caprica-Six under the pretense of telling her that her petition to see Hera Agathon has been denied, if she feels guilty about the attack on the Colonies and how she deals with that, Caprica-Six tells him that she is just as human as him. She tries to offer Tigh the salvation she thinks he is seeking, but Tigh refuses and leaves. However, he returns later and Caprica tells him that Cylons can't simply switch off their pain, but found a human way to get rid of it. She acknowledges her role in the fall of mankind and the betrayal of the man she loved, but says that she needs that pain to find clarity and learn who she really is. Caprica-Six tries both tenderness and violence to share some of that insight with Tigh, but he refuses her (Escape Velocity). Often in her moments of tenderness, she appears to Tigh in the voice and face of his late wife, Ellen.
It is later revealed that Tigh did have a physical relationship with Caprica-Six during his many visits to her cell. A furious Admiral Adama informs Tigh that Dr. Cottle discovered she is pregnant and that Tigh must be the father (Sine Qua Non). Virtual Six's claim that a child would be born in Agathon's cell (Home, Part II), gains a new dimension in light of this development. It was initially supposed she was referring to Hera, but Hera was neither conceived nor born in that cell. However, Caprica-Six's child was at least conceived there.
Upon arriving at Earth, Caprica-Six is released from captivity, as a beneficiary of the general amnesty granted by President Adama to the "final four" Cylons.  As the landing party stands on Earth in shock, after discovering that it has been destroyed, she walks towards Tigh and touches him (Revelations).
During Gaeta's Mutiny, Caprica-Six is joined in her cell by Helo, Sharon Agathon, their daughter Hera, and Samuel Anders. She surmised that the humans revolted because they felt threatened by her unborn Cylon child and Hera, a Cylon hybrid. She did not realize that the revolt was caused by the mutineers fear of the rebel Cylons boarding Colonial vessels and sabotaging their FTL systems.
After Ellen Tigh return to the fleet, she, Tory Foster, and Galen Tyrol vote to leave the fleet and go off with the other Cylons, along with Caprica-Six. Saul Tigh refuses to go. Immediately after he tells Caprica-Six that she can go without him, her pregnancy goes into distress. She is taken to sick bay, where Saul professes his love for both her and Ellen; unfortunately, the pregnancy ends in a miscarriage ("Deadlock").
Rescue of Hera Agathon and rekindling of relationship with Baltar
After her failed pregnancy, she seems to have fallen out with Tigh as Baltar offers her a home with him. She refuses stating that she has changed but he hasn't. Later when Admiral Adama calls for volunteers to rescue Hera Agathon, Caprica-Six volunteers.
During the Battle of The Colony, Caprica-Six is assigned to be part of the reserve team alongside Baltar who is surprised to see her and says she shouldn't be there, but she points out she's been in more battles than he has. She is proud of him for staying and she thinks that pride in him was what was missing in their relationship. The two kiss, and are interrupted by Virtual Six and Virtual Baltar who both can see. Caprica-Six and Baltar are surprised that the other can see them. The two defend Galactica from Cylon boarders. After being forced to retreat, the two find Hera and in a parallel of the Opera House Prophecy, carry her through the corridors to CIC, where they find the Final Five in a similar position to the one they took in Six's visions. When Cavil captures Hera in CIC, Caprica-Six is one of those holding a gun on him while Baltar and Tigh diffuse the situation. Later, she and Baltar move to the habitable planet that the Fleet finds and settles on, which is named Earth. They watch Hera, wondering if she'll be alright, and receive a final visit from Virtual Six and Virtual Baltar who are really angels of God. They reveal that Caprica-Six and Baltar's destiny was always to protect Hera and now that that's done, their role is over. God's plan is never over, but Virtual Baltar assures them that their lives will now be less exciting, before both Virtual Beings disappear for the last time. Caprica-Six heads off with Baltar to start a new life together as farmers using Baltar's knowledge from growing up on a farm.