Has to be 'The Atlas Affair' by Nagorak. Which is also part one of a three parts series, and they're honestly quite good.
Basically, you are investigating pirate affairs in whichever sector it takes place in (Don't quite remember the exact details). Once you've discovered who the pirates are you have to stop them. But something goes wrong. *uh-oh...*
It has a great story, and whichever choices you make effects the end-game. It's amazingly done, and it is, in my opinion, the best foundry mission out there.
All time favorite.
Sometimes I think something else has become my favorite, then I replay Polmar Ree and realize I was mistaken. City of the Polmar Ree gets me right in the feels. Every time, even though by now I know exactly what's coming.
The Infinite Realities series by Captain Revo. 6-part story involving the mirror universe and another alternate reality where the Borg won in TNG: "The Best of Both Worlds" and the rest of the AQ powers united to fight back. Also ties in story bits from Deep Space Nine.