The Equestrian Mortal Kombat tournament determines who rules Equestria: The Lunar Republic or the Solar Empire. Since Luna's banishment, the tournaments were postponed, but now that they have restarted, the Princesses need new fighters to represent them in combat.

This time around, two new clans have threatened Equestria; The Lin Kuei and the Shirai Ryu. With contestants entering from these groups, the fate of Equestria now lies outside the two Princesses…