I can't find this fic that's fairly widely known.

[myself365.livejournal.com]

Jim is mob boss. I seem to recall everyone else is still in Star Fleet.

Spoilers: The twist is that Jim is actually undercover to take down the mob.
I'm pretty sure he gets shot and they make everyone else think Bones is dead.

Edit: Thanks so much, that's it!

Comments

[(Anonymous)]

Here it is!

http://archiveofourown.org/works/826785/chapters/1570059