Another Sharon, who is fully aware of her true nature, also appears in the series. This Sharon also seems to possess memories of the experiences of Boomer, including memories of her relationship with Tyrol.

She first appears when she joins Lt. Karl 'Helo' Agathon after he is stranded on the Cylon-occupied planet Caprica. She pretends to be the "original" Sharon who had returned to help him, when in fact she is working with the other Cylons on a breeding experiment. While her intentions at the beginning of the experiment are strictly part of the Cylon plan, she eventually falls in love with Helo, and tries to help him escape from the other Cylons. Helo discovers her true identity when he sees another Number Eight copy on Caprica (who attempts to kill him but is shot by Sharon), but Sharon eventually convinces him that she loves him, and also reveals that she is pregnant with his child. This pregnancy is the first successful attempt at a humanoid-Cylon/Human Hybrid, and as a result is of great importance to the Cylons.

While on Caprica, Sharon and Helo encounter Kara 'Starbuck' Thrace, who realizes that Sharon is a Cylon "copy" and attempts to shoot her, but is stopped by Helo. Sharon flees in Starbuck's captured Cylon Raider, casting doubt on her intentions, but returns later to help Helo and a human resistance movement rescue Starbuck from a Cylon facility. Though only Helo trusts her, the group allows Sharon to accompany them as they rejoin President Laura Roslin's portion of the Colonial fleet, separated from Galactica.

Sharon's life is again threatened upon her return to the Colonial fleet, after William Adama's attempted assassination and Boomer's death, first when Lee 'Apollo' Adama attempts to shoot her and Helo intervenes, and second when Roslin orders her thrown out an airlock until she uses her knowledge of the Tomb of Athena on Kobol as leverage. She demonstrates her loyalty several times in defending the group from Cylon ambushes during the trip to the tomb, even though she is chained and not distrusted.

Sharon's reunion with other Galactica personnel on Kobol is also tense, as Commander Adama initially attempts to strangle her, while her relationship with Tyrol is complicated by the events involving Boomer, as well as her romantic involvement with Helo. Despite Adama's animosity, she saves his life by exposing a plot to kill him by one of Tom Zarek's followers. She tells them, "I'm Sharon, but I'm a different Sharon. I know who I am. I don't have hidden protocols or programs lying in wait to be activated. I make my own choices, I make my own decisions, and I need you to know this is my choice." Still, she is imprisoned upon returning to Galactica and is treated as an enemy by all but Helo and Tyrol.

Sharon again demonstrates her loyalty when the Galactica is threatened by a Cylon computer virus, and uses her Cylon capabilities to instead turn the virus against the large approaching Cylon raider attack force, allowing the Colonial pilots to completely destroy the enemy. Although she performs this action, she seems conflicted and pained by its repercussions (mainly the subsequent slaughter of raiders). This event causes Roslin and Adama to re-evaluate their attitude towards her, and earns her significant trust. She makes several other valuable contributions to the human cause, offering intelligence and advice on various Cylon situations.

When the Battlestar Pegasus is reunited with the Colonial fleet and its commander, Admiral Helena Cain, discovers Sharon's presence, Sharon is turned over to Pegasus's "Cylon Interrogator", Lt. Thorne. Thorne beats Sharon and attempts to rape her, but is killed in the process of Helo and Tyrol intervening.

Sharon's unborn hybrid child is threatened when Roslin orders the pregnancy terminated, outraging Sharon and Helo, but later relents when blood from the fetus cures her terminal cancer. The pregnancy is allowed to continue, and in "Downloaded", Sharon gives birth to her child prematurely, via an emergency caesarean section. The daughter is named Hera. As the baby is deemed a risk to the Fleet if raised by her Cylon mother, Hera's death is faked by Dr. Cottle, and she is given to a human mother to raise, unbeknownst to either Sharon or Helo. Told that Hera died from breathing complications, Sharon assumes that Hera was killed by the Galactica crew and attacks Dr. Cottle and turns on Helo. She later helps navigate a mission to rescue survivors on Caprica, but her loyalty is again called into question when she chooses not to inform the Colonials that one of the survivors is a Cylon.

In Season 3's "Occupation", it is revealed that during the year-long gap between the events of seasons 2 and 3 Sharon and Helo were married, and Sharon took Helo's surname, Agathon. With the Galactica in need of pilots after the return of the Cylons, and having earned the full trust of Admiral Adama, Sharon is sworn in as an officer in the Colonial Fleet, gaining the rank of Lieutenant. She is sent back to New Caprica as the liaison between the Galactica fleet and the resistance effort on the ground as a precursor to an attempt to free the subjugated humans from the occupying Cylons. Adama explained that she was the ideal agent, since Centurions cannot tell her from any of the other Eights. Sharon infiltrates the Cylon Base, and is able to steal the keys for the civilian ships, thus making Adama's escape plan possible. When leaving with the keys, she encounters D'Anna Biers, a Number Three, who informs her that her child Hera is still alive.

After the successful rescue of the colonists, Sharon gains a measure of acceptance among the Galactica's pilots. When Racetrack refers to her by the old call sign 'Boomer', she replies that 'Boomer' was somebody else. The other pilots in the rec room offer suggestions for a new call-sign, many of them affectionately teasing her for being a Cylon and suggesting names like "Toaster" and "Titanium". "Hot Dog" suggests Athena, the goddess of wisdom and war, and Sharon proudly accepts it.

Athena displays the ability to identify individual Number Eight copies, identifying Boomer when she arrives aboard Galactica to negotiate with Admiral Adama. When Colonel Tigh bars Boomer from the meeting, she repeats Number Three's message that Hera is still alive, but ailing, aboard a basestar. Adama confirms this information in a tense conversation with President Roslin, and both Athena and Helo express feelings of outrage that their child was stolen from them. Athena demands that she be able to see her daughter.

As there is no way that Adama would let her visit the basestar, Athena is shot by Helo and downloaded on the Cylon resurrection ship. Caprica-Six brings Athena to the room on the basestar where Boomer is caring for the child. Athena insists that Hera's illness could be cured by the human doctors on Galactica, a possibility that neither Six nor Boomer wish to consider. Athena and Boomer have a heated discussion on the fate of the child, with Boomer expressing a desire to abandon the experiment entirely and kill the child. Before Athena can intervene, Six promptly kills Boomer for considering the death of the child. Before their actions can be discovered, Six whisks Athena and Hera to a raptor, and the trio escape to Galactica.

Sharon's abilities as a pilot are recognized and she is given the most important missions for Raptor pilots. Sharon discovers that she, Hera, President Roslin and Caprica are sharing the same dream but is unaware of what it means.

Athena was present when a thought-dead Starbuck returns to Galactica. She is eventually chosen to serve aboard the Demetrius, a ship under the control of Starbuck, with Helo, Gaeta, Anders, Seelix, Mathias, and several others, in an attempt to find Earth. As Starbuck becomes increasingly irrational, Athena becomes more and more frustrated. After her friend Mathias is killed inspecting a Cylon ship, Athena encourages Helo to take command of the mission. The crew was given a deadline to meet back up with the fleet- failure to do so would result in the fleet jumping away, lost to the Demetrius forever. When Starbuck decides to ignore the deadline and travel to a Cylon basestar to see the hybrid, a mutiny occurs. Athena grabs Starbuck in a choke-hold, but when Anders shoots Gaeta Starbuck decides to take Leoben, Anders, Jean Barolay, and Athena to the basestar on a Raptor.

While preparing to leave for the basestar, Leoben freaks Athena out by telling her that the other Eights talk about her all the time. She begins to understand what he means after arriving at the basestar: a dozen or so Eights swarm to her and ask her to lead a rebellion against the Sixes. Athena expresses disgust with the other Eights for being flakes. She tells them that they have to pick a side and stick to it or they won't have anything. The Eights are left confused and hurt. Elsewhere on the ship, a Six has attacked and killed Jean Barolay (who brutally killed the Six). Athena demands that the Six be punished for the murder. Later, a fellow Eight is killed by a Centurion, which was, in turn, killed by Athena and Starbuck. As the Eight dies, she reaches out to Athena, apologizing for their earlier encounter. Athena reaches to take the Eight's hand, but pulls back at the last second and backs away. She seems distressed.

While preparing the Raptor and basestar to jump back to the Demetrius, Natalie remarks that Hera must be beautiful, a comment that disturbs Athena. After reuniting with the Colonial Fleet, Athena begins to dream about the Opera House again. She wakes to see Hera standing next to her bed, saying "bye-bye." Later, after returning from CAP, Athena looks through Hera's drawing book and realizes Hera has drawn the numeral 6 repeatedly, as well as a Six wearing a red dress. When she turns to ask Hera why, Hera is gone and the door is sitting open. Athena runs through the hallways calling for her daughter, having flashes of the Opera House dream. Becoming increasingly panicked, she eventually finds Hera with Natalie. Athena pulls her weapon and demands that Natalie get away from Hera. Hera, frightened, clings to Natalie's leg, exactly as Hera did to the Six in the Opera House dream. Panicking, Athena asks Tyrol to move Hera away. She then shoots Natalie twice. She's taken into custody with Marines, who later take her to Adama's quarters. She attempts to explain about the vision but Adama has her sent to the brig. Later, Tigh has Hera sent to stay with Athena in the brig, as Adama ordered.

Athena is later reunited with her husband, and Earth is discovered. She is seen walking with Helo through the carnage, Starbuck with them. The Agathons are not seemingly as affected by the discovery of Earth as the others; home for them was never a place, but each other - it had to be. When tensions in the fleet lead to a coup, the Agathons are targeted by anti-Cylon Colonials; they are rounded up, Helo is beaten unconscious, and taken to the brig. They are placed with the other Cylons - Tigh, Anders, Caprica - and are eventually rescued by Starbuck and Lee. They join Adama in putting down the rebellion and taking back the ship.

Athena - during a strenuous time aboard the ship between the repairs being made, and a dearth in capable pilots after many were imprisoned for mutiny - is attacked by Boomer. She is beaten, stripped, bound and gagged, then hidden in a bathroom stall. When she gains consciousness, she sees Boomer having sex with Helo (who believes he is sleeping wit his wife). She is eventually able to free herself, and alerts Helo to what has really happened. When we next see Athena, she is completely devastated by the loss of her daughter and is consumed by the vision of the Opera House (which is also still plaguing Caprica and Roslin). She is alternately unresponsive and hostile to Helo. She remains in their quarters and becomes despondent, even when a rescue mission is announced.

As the mission begins to take shape, Athena seems to become more hopeful. She, Helo, Starbuck, marines, and free Centurions board The Colony to find Hera. However, it is Boomer who finds them; she brings them Hera. Athena tells her it doesn't change what she did and Boomer agrees. After a signal from Boomer, Athena opens fire and kills Boomer. When the rescue party returns to Galactica, a battle is already underway there. 145's and their Centurion force have boarded the battlestar and a 4 (Aaron Doral's model) shoots Helo. Hera, frightened, runs away and Helo tells Athena to leave him behind and find their daughter. As Athena chases Hera, the Opera House vision becomes a projection. Roslin had begun to experience it as well, and encounters Hera who eventually runs away. Athena and Roslin, both chasing the child, encounter one another and then both spot Caprica holding the child exactly as the vision showed. But Caprica, unaware of Athena, shuts the causeway and seals it. Athena continues desperately to get to her daughter.

Eventually, Athena is reunited with Hera in the CIC (the Opera House). Athena, Hera, and Helo are last seen on Earth 2, discussing the new life they are going to build.