Starter Villain might also scratch that itch for you, but to be honest, I’m just a big Scalzi fan. Kaiju Preservation Society and When the Moon Hits Your Eye were a lot of fun too.

Might not be an exact fit, but maybe Old Man’s War by John Scalzi. It’s not a mystery per se, but there is definitely an element of “what’s actually going on here” for the main character to sort out.