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What no one understood was that it wasn't the poverty that bothered Simon the most. It wasn't the backwater planets and eating tasteless protein every day, or the lack of privacy and luxury. He could cope with the danger and wearing the same five shirts over and over because he didn't have the opportunity to buy more, much less the money. Being wanted was awful, a nearly constant fear crawling along his normally rock-steady nerves, but after months of searching for River it was almost a relief to be the hunted rather than the hunter.
He could handle Jayne's ignorant cruelty, and Mal's stubborn disrespect, and the affection Kaylee offered and he wasn't sure how to return. The primitive conditions and equipment were frustrating, but nothing he couldn't adapt to, and there were always plenty of injuries and illnesses to keep him occupied, even if he didn't get anywhere near the wealth and respect he was used to in return. River's illness was an entity to itself, a foe he barely knew how to combat. But he was determined to make progress, to help her, and part of that was coming to terms with the fact that she did need help.
No, what bothered Simon the most about their situation was when he had to hurt or kill someone else. He was a doctor, sworn to do no harm; he was supposed to be making people's lives better, not ending them. It went against every instinct, every trained response, to intentionally strike out with the intent to cause harm to another sentient being... but these people wanted to hurt River, to take her back where she would be tortured, and he couldn't let that happen.
Simon is River's big brother, and he would do *anything* to keep her safe.