DC and co-creator of the Mortal Kombat franchise, did confirm that the player would have the ability to play as all the characters in the story mode at one point during development, but the story mode instead had a few characters not having their own story arcs. Mortal Kombat vs. DC Universe also contains a mode called 'Kombo Challenge'.
This aspect of MK vs. DC is individual to the Versus and Story modes, where players must perform ten precreated combos of increasing difficulty. DC features a story mode, playable from two different perspectives. The perspectives consist of one segment from the DC Universe side, and one from the Mortal Kombat side, each split up into various chapters. Depending on which side players choose, the characters see characters from the opposite universe as the invaders of their own. Ed Boon, creative director of MK vs. DC and co-creator of the Mortal Kombat franchise, did confirm that the player would have the ability to play as all the characters in the story mode at one point during development, but the story mode instead had a few characters not having their own story arcs.