When the Galactica was being decommissioned, you couldn't expect much propriety among the ranks of the soon-to-be-reassigned, so no one cared that Lieutenant Sharon Valerii, Raptor pilot, call sign Boomer, was frakking the Deck Chief, Galen Tyrol. After all, the starboard hangar deck had been turned into a gift shop. The military was about to hand the ship over for education and tourism use; fraternization wasn't that big a deal.
And then the war happened, and Boomer started to crack. Gaps in her memory, strong evidence of wrongdoing on her part, and the Chief, always reliable in troubled times, protecting her from everything, even from herself. He didn't want to believe she could be capable of sabotaging the fleet's water supply, so he did what he had to do to prevent her from being accused of the crime. Their relationship was suddenly under the microscope for being against military protocol, so they moved in shadow, met in secret, and he protected her still, to the point of perjuring himself.
But what Chief Tyrol will take on his own conscience, he cannot abide seeing others carry in his stead. When Specialist Socinus wound up in the brig over trying to keep the Chief and Boomer's secret, it sickened the Chief. Perhaps seeing Boomer's easy smile, as if she was unaffected by Socinus' sacrifice, was what pushed the Chief over the edge, driving him to end their relationship. It didn't help, of course, that he was beginning to doubt her on other, more disturbing levels. He had been willing to write off her apparent guilt for the water tanks as a frame-up, but her insights about, and lullabies to!, the Cylon Raider were unsettling to him.
When it was at last known to all in the fleet that she was indeed a Cylon, he was thrown in the brig based on his past relationship with her. Her guilt, horror, and self-loathing at that point were amplified when he spat the words, "You're a machine. I'm not." (talk about irony) Yet in her clarity of despair, she was able to experience, and to express her love for him again without reservation.
Death came quickly to her after that, but she died in Chief Tyrol's arms, perhaps reassured in that moment that he did still love her, whether or not he could reconcile that with all he now knew.
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