Didn't NRS confirm that every playable character has a chapter in story mode? Because if that's the case then the actual Doomsday will have to show at some point for his chapter.
"According to the developers, the story mode will be peppered with small interactive mini-games like this to break up the action and add a little variety. While this particular idea is new, most of the formula sticks to the setup found in Mortal Kombat: each chapter of the story mode follows a particular character for three to four increasingly challenging fights before placing you in control of someone new. The matches and events are all preset, so you never select a fighter or a difficulty level. If you keep losing a particular match, the enemy AI just gets a little dumber until you eventually overcome."