To try to sum it up, the main rationale is that during the pilot ep when the Reaver ship is near, Inara takes out something that looks medical. Joss says during the commentary that it is *not* a suicide kit and that it's a clue to Inara's secret. So if it's not a suicide kit, is it some medicine she takes to deal with the symptoms of a medical condition. There's also the scene in Out of Gas where she and Simon are talking and she says, "I don't want to die at all". She doesn't look at him as she says the line and in fact seems absorbed in something else entirely. (In fact, I can't remember if we were also told in DVD commentary that that scene had a clue too).
So those are the main pieces of evidence -- you couple that with her unwillingness to get attached to anyone, you may have an answer as to why a top class companion is on a ship like Serenity.
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To try to sum it up, the main rationale is that during the pilot ep when the Reaver ship is near, Inara takes out something that looks medical. Joss says during the commentary that it is *not* a suicide kit and that it's a clue to Inara's secret. So if it's not a suicide kit, is it some medicine she takes to deal with the symptoms of a medical condition. There's also the scene in Out of Gas where she and Simon are talking and she says, "I don't want to die at all". She doesn't look at him as she says the line and in fact seems absorbed in something else entirely. (In fact, I can't remember if we were also told in DVD commentary that that scene had a clue too).
So those are the main pieces of evidence -- you couple that with her unwillingness to get attached to anyone, you may have an answer as to why a top class companion is on a ship like Serenity.