Shang Tsung decided that he would fight and conquer Middle Earth for Shao Khan. A Tournament was put into place of Mortal Kombat. Trolls and various fighters chose to take part of the Tournament. One of the battles was Shang Tsung against the mighty WitchKing. Shang Tsung is considered powerful enough to fight the WitchKing despite the Prophecy shield.
The Witch King has his powerful magicks to wield in the fight, and Shang Tsung has many souls to draw from for power, maybe even some from Middle Earth, and the Mkers he has killed trying to stop him from invading ME(take your pick).