Short stories are not immune from this good advice. Some stories are not so physical, but what violence are you wreaking upon your protag's soul? Has he undergone a trial that will change him, and maybe the world around him, forever? Has he sacrificed? Has he fought against all odds for what he believes, or what you want him to believe?
He needs to lose his sword, crawl through the mud in a violent thunderstorm, everyone dead or dying around him! He has to be covered in blood and devoid of all hope. Light should be cracking through the pearly gates; his ancestors must be waving from the tunnel of white light. He must be so weakened that the antagonist not only holds all the cards (and said sword), but has plenty of time to decide how to play them. And then, still, after all that, the protag must prevail--mostly alone.
Once you get to know your protag well, the Black Moment is fairly easy to construct. Simply take away what he wants most in life, and make him fight like hell to get it back.