Moriarty has enemies I'm sure. So maybe once when one of his cases as a consulting criminal doesn't go so well the unsatified client comes back and takes revenge on him. Moran is there too and tries to protect him but they knock him out.
They shoot Moriarty in the stomach with Moran's gun then torture him, humiliate him, rape him and leave him there. Moran calls the ambulance but doesn't remain there as he is a wanted criminal too.

Sherlock takes the case (because I do think he misses Moriarty if something happens to him and he needs to know what happened), surprises and upsets everyone because he would rather choose the case of that madman than a case of an innocent person. Not to mention that John begins to see too much emotions boiling up inside of Sherlock during the investigation which wouldn't fit with Sherl's character.

Sorry for long prompt... Just can't take it out of my head...