Throughout the Mortal Kombat universe, the warriors were growing too strong and numerous for the realms to handle. The warriors' powers threaten to utterly destroy the fabric of the MK universe. These warriors clashed in a single battle royale that would threaten to rip apart reality and bring about the apocalypse. Without warning, a pyramid rises from the ground, and the tip bursts into flames, attracting the warriors' curiosity to see what it was. The kombatants fought one another to get to the top, while Blaze revealed himself to them. The firespawn was created by the Elder Gods to destroy as many fighters as possible in order to save the realms from Armageddon. This would be the warriors' last battle, their last chance to prove that they are worthy of surviving, while many others will perish. This will be the final battle for Mortal Kombat, the battle that will determine the fate of the realms...

Originally, Armageddon was billed as featuring every single fighter from the six main installments of the franchise thus far. Later, developers went on to add characters that were exclusive to the renditions of such titles (for example, Chameleon from Mortal Kombat Trilogy) to the final roster. Still, however, Armageddon does not include every single fighter that has appeared in the franchise. Some characters that have appeared in the adventure titles - Mortal Kombat Mythologies: Sub-Zero, Mortal Kombat: Special Forces, and Mortal Kombat: Shaolin Monks - are not in Armageddon. Also absent was Khameleon, a secret character who appeared in the Nintendo 64 version of Mortal Kombat Trilogy; however, due to fan complaints, she is now a playable character in the Wii version of the game.

Only two characters, Daegon and Taven, are new to the series, while Sareena makes her playable debut on non-portable consoles and Meat makes his debut as a legitimate character.

In addition to the choice of over sixty characters, Armageddon gives players the ability to design and use new fighters in the game.  From the number of options, there are potentially thousands of different combinations available. During production, the game offered at least fourteen different character classes, which include humans, Tarkatans, Mercenaries, Black Dragon Members, Ninjas, Retro Ninjas, Geisha Assassins, etc. However, after the game's release, only one preset was available to the two genders, Sorcerer to Male, and Tarkatan to Female. Although the clothing of each class is still available, it must be individually unlocked, and cannot be preset. All these presets can be unlocked by unlocking each piece of clothing that makes up that class. The preset will then appear under the preset menu.  Players can give their character a unique fighting style, by changing their stance and assigning different attacks to the buttons on their controller. There is a range of swords and axes (the only weapons available) and special moves to choose from. Most moves and costume items need to be purchased with koins earned in the game's other modes, though some moves and items are available for free from the beginning.  The fighters can also be given their own storyline. If a player uses their creation to finish a single player game, they will see the ending that the player designed for them, although the ending will cut off after roughly twelve lines or if the last line consists of one word. They can also be used in multiplayer games and online, using the PlayStation 2's online capability or Xbox Live. The ending that the game shows is the same text that the player inputs as the fighters biography.