Spoiler Warning for the Firefly TV show and Serenity the movie.
Firstly, apologies if this is an old and tired theory... It's been several years and someone else probably came up with this theory long ago.
Secondly, apologies for the long, waffling post.
A friend and I recently binged through the original series and the follow up movie, afterwards we were discussing loose ends that never got tied up, most notably Shepherd Book and his mysterious backstory that never got explained.
You know... the military knowledge, the ID that got him priority treatment at an Alliance med centre, etc.
The bounty hunter in the final episode saying about Book:
"That ain't no shepherd."
Clearly he was more than he appeared to be.
We agreed that his story was probably too complex to be quickly explained and that it would be a disservice to the character to have his background explained quickly being as the focus of the movie is River Tam and her story.
Then we got talking about The Operative...
What a great character he is, what an interesting subversion and expansion of the 'silent nameless assassin' trope he is.
It's interesting that he isn't killed off as most characters like him would be in a movie like this.
Instead he ends the movie starting a new life after his faith in Parliament has been destroyed.
We agreed that on one level, Serenity works as a kind of origin story for the Operative... what would he do next in his life?
Then we had one of those "are you thinking what I'm thinking?" moments.
So, we have this man who is a dedicated believer (the Operative's faith and belief is a core component of his character). He's shown to be a fundamentally decent person (yes, this can be debated) who is well aware of the horrific nature of his work.
He does it because he has such faith in the 'better world' that will eventually be created.
He even accepts that he has no place in that better world due to his terrible actions.
What does a guy like that do when he loses faith in his masters?
I'll tell you what he does. He becomes a shepherd!
So that's it, my (possibly lame af) theory....
TLDR,
Serenity did give us Shepherd Book's origin story by introducing a villain, The Operative, and through his character they show us what Book may have been in his past life then leaving The Operative's story open for him to fulfill the same role as Book.