Sherlock is assaulted while investigating a case in a rough neighborhood. He is convinced them men who did it were hired by Moriarty, though there's no indication of that.
The story, seen through John's eyes, deals with Sherlock's emotional state as he recovers from the assault. John's concern - and anger - are also constantly present. The assault happens at a time when he and Sherlock have been sleeping together sporadically for a while, and John's not sure what level of comfort he can offer.
Outstanding moments in the story:
John and Sherlock at the crime scene - a filthy alley - where Sherlock ditches John in order to go interview other victims;
Sherlock confronting one of the men in the police interrogation room, and realizing that the man wasn't hired by Moriarty at all;
the courtroom, and the sobbing woman;
John dropping the vase of roses out the window.
The emotions in the story are painful, as expected. But the relationship between John and Sherlock is wonderful, with John trying to take care of Sherlock however he can, and Sherlock aware of that.
Special notice to the fact that Sherlock hides John's gun to keep him from going after the thugs in the courtroom.
Everything a Bit Broken, by thingsbaker