In this arcade-style fighting game, both DC and Mortal Kombat universes are represented by 10 champions each, and one "boss" character, for a total of 22 fighters. Play is similar to the 2D Mortal Kombat games (with some 3D elements), focusing more on the special move aspect than the complex combos found in the previous three games (Deadly Alliance, Deception, Armageddon).

As with any Mortal Kombat game, Fatalities are still present for the Kombatants and villains, though slightly toned down to meet the DC standards of heroes such as Superman and Batman keeping to their moral code and not killing their opponent. As a result, the DC heroes perform "Heroic Brutalities", which effectively put their opponent out of commission.

After Shao Kahn's invasion of Earthrealm is halted by Raiden's forces of light, Raiden blasts and sends Kahn through a portal. At exactly the same time on Earth, Superman stops Darkseid's Apokoliptian invasion by blasting Darkseid with his heat vision as he enters a boom tube. These acts do not destroy either of them, but merge them into Dark Kahn, and causes the DC and Mortal Kombat universes to merge. As this happens, the characters' abilities fluctuate, causing violent "rage" outbreaks that are actually the feelings of Dark Kahn being infused in the characters from afar. With each world thinking that the other is responsible for the merger, they fight each other until only one fighter from each side remains.