I've been looking for this story off and on for the past year, to no avail; I think it's pretty recent, published in the past 20 years or so. I read a lot of short story anthologies but I can't find this one.
The main character (a mercenary type) and side-kick (who IIRC is a human who's in the body of a dinosaur... maybe a velociraptor?) are enslaved by some sort of alien hive-mind who's using them to locate a powerful weapon.
They travel around in a stolen ship from some other alien race (IIRC caste-based, maybe crab-like?) that has a space-elevator they use to descend to planet surfaces and conduct deals in their effort to locate the weapon.
The story starts in media res, with the main character + side-kick in the middle of a deal gone bad (their trading partners were trying to rip them off and steal their ship; it doesn't end well for them).
The main character has to periodically contact the controlling hive-mind and endure agonizing psychic debriefings.
In the end (spoilers!) the main character finds the weapon and turns it against the hive-mind, and realizes he's a clone (the original was kept near the hive-mind in some sort of stasis chamber).
Anyway, I really loved the mood of this story and I'd like to reread it but I can't find it no matter how many Year's Best anthologies I scour!