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Choice
I think the biggest reason Sharon has a problem fitting into the fleet isn't that she's merely a cylon, but that she is a copy like Boomer, and everybody associates her with the atrocity of Boomer's act against the Commander.
After rescuing Helo and Starbuck from Caprica and rejoining the human fleet outside of Kobol on Roslin's ship, Roslin and Apollo both want Sharon dead and take actions to try to make it happen - Apollo with a gun, and Roslin ordering that she be thrown out the airlock. Apollo kept yelling that Boomer shot his dad, and while Sharon was being dragged toward the hatch, she yelled, "It wasn't me! That wasn't me!"
That was the first of many times that Sharon had to take a fall for Boomer's actions. She ended up living because she was able to make herself valuable with her knowledge of the scriptures, Kobol, and in particular the Tomb of Athena. With the majority of humans against her though, she still had a lot to prove. To them, she was as Apollo said, trash.
It's good to see you again Kara. Thanks for bringing in the trash.
Sharon separated herself from Boomer by helping the humans on Kobol by destroying some Centurians and helping them escape from fire.
It was also on Kobol that one of my favorite scenes ever on the show took place. A plot by one of Tom Zarek's friends to kill Apollo and Commander Adama was spoiled by Sharon when she turned the gun on him instead. He had given her a gun thinking he was manipulating Sharon by saying that she'd be killed like Boomer as soon as she made it to Galactica. She saved his life even after he tried to strangle her to death for Boomer's attempt to assassinate him. It probably would have been her only opportunity for the fleet to see that she wasn't Boomer, and she took it.
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.
Adama still looked at her as an enemy, and when they made it back to Galactica, she was put in the cell built for Boomer, visited only by Helo and Tyrol who treated her as a person.
It took a lot more for Adama and the rest of the fleet to accept Sharon as an individual and not associate her with Boomer. Before she got the name of Athena, members of the fleet even called her Boomer, to which she corrected them each time. Sharon was finally able to win the fleet over however, with her military efforts.
Silent Lucidity was created and is maintained by me, Todd, and is part of Dragonzord,net. This shrine was made for fun and is entirely non-profit. It is made up of my own personal opinions and perception. Sadly, I don't own the Eights or Battlestar Galactica. They are property of SciFi. Please don't sue me.