Really good writing, and a great character
Read the story now
Nina is a great character.
This is really good writing. It keeps you engaged, and there's foreshadowing that you only understand once you've read the whole thing. I didn't see the twist coming at all, but as contrived as it could have been, I think it actually really works.
A few tiny things:
You might want to mention in the summary that there are spoilers for Serenity, just in case people haven't seen it yet.
At the beginning, “new pilot” should be “a new pilot”. And then you could do with a blank line between that paragraph and the next, as with the rest of the script.
In the paragraph before the first page break, there are several dashes. These should really have a space either side, to make it easier to read.
At the end, I don't feel like Mal would put his head in his hands. The rest of the description of Mal there probably works, though.
The name Nina initially made me think of an existing Firefly character, Inara's friend (who's actually called Nandi). My instinctive thought was that the story was about her being the new pilot, which didn't obviously seem like it would work. Also, the summary could do without the cryptic introduction. Just cut out “It's a while before she arrives on Serenity. Or:” from the summary. Thankfully, I read the story anyway, and was pleasantly surprised.
In the summary, it's not “the Serenity”, it's just “Serenity”. An easy mistake to make, but Inara actually makes the point in one of the episodes. :)
A great story, very well written. Congratulations.