The series takes place in a fictional universe that consists of six surviving realms which, according to in-game backstories, were created by the Elder Gods. The Mortal Kombat: Deception manual described the six realms as: "Earthrealm, home to such legendary heroes as Liu Kang, Kung Lao, Sonya Blade, Johnny Cage, and Jax, and also under the protection of the Thunder God Raiden; Netherrealm, which fiery depths are inhospitable to but the most vile, a realm of demons and shadowy warriors; Outworld, a realm of constant strife and where Emperor Shao Kahn claims this realm as his own; Seido, The Realm of Order, whose inhabitants prize structure and order above all else; The Realm of Chaos, whose inhabitants do not abide by any rules whatsoever, where constant turmoil and change are worshipped here; and Edenia, which is known for its beauty, artistic expression, and longevity of its inhabitants." The Elder Gods decreed that the denizens of one realm could only conquer another realm by defeating the defending realm's greatest warriors in ten consecutive Mortal Kombat tournaments.
The first Mortal Kombat game takes place in Earthrealm where seven different warriors with their own reasons for entering participated in the tournament with the eventual prize being the continued freedom of Earthrealm. Among the established warriors were Liu Kang, Johnny Cage, and Sonya Blade With the help of the Thunder God Raiden, the Earthrealm warriors were victorious and Liu Kang becomes the new champion of Mortal Kombat. In Mortal Kombat II, unable to deal with Shang Tsung's failure, Outworld Emperor Shao Kahn lures the Earthrealm warriors to the Outworld where the Earthrealm warriors eventually defeat Shao Kahn. By Mortal Kombat 3, Shao Kahn revives Edenia's (now a part of his Outworld domain) former queen Sindel in Earthrealm, combining it with Outworld as well. He then attempts to invade Earthrealm but is ultimately defeated by the Earthrealm warriors again. After Kahn's defeat, Edenia was freed from Kahn's grasp and returned to a peaceful realm, ruled by Princess Kitana. The following game, Mortal Kombat 4, features the former elder god Shinnok attempting to conquer the realms and attempting to kill the thundergod Raiden. However, he is also defeated by the Earthrealm warriors.
In Mortal Kombat: Deadly Alliance, the sorcerers Quan Chi and Shang Tsung join forces to conquer the realms and subsequently become the antagonists. By Mortal Kombat: Deception, after several fights, the sorcerers emerge victorious having killed most of Earthrealms' warriors until Raiden steps forth to oppose them. The Dragon King Onaga, who had been freed by Reptile at the end of Mortal Kombat: Deadly Alliance, had deceived Shujinko, the protagonist of Mortal Kombat: Deception, into searching for six pieces of Kamidogu, the source of Onaga's power. Onaga then confronted the alliance of Raiden, Shang Tsung, and Quan Chi and thus obtained Quan Chi's amulet, the final piece of his power, becoming the antagonist. Only a few warriors remained to combat against the Dragon King and his forces. Shujinko eventually triumphed over the Dragon King and removed his threat to the Mortal Kombat universe.
In Mortal Kombat: Armageddon the catastrophe known as Armageddon starts. Centuries before the first Mortal Kombat, Queen Delia foretold the realms would be destroyed in an event known as Armageddon. King Argus had his sons, Taven, the protagonist of the game, and Daegon, put into incubation who would one day be awakened to save the realms from Armageddon. In the end, however, because Blaze's design has been corrupted by Onaga's holy men, Taven's victory over Blaze does not destroy the combatants or strip them of their powers, instead increasing the powers of the fighters, potentially exacerbating the onset of Armageddon. As a result, Taven will make it his duty as a new god to delay Armageddon until a solution can be found.
In Mortal Kombat (2011), it is revealed that the battle between the warriors of the six realms culminated into only two survivors: Shao Kahn and Raiden. Badly beaten, Raiden had only one last move he could make to prevent Shao Kahn from claiming the power of Blaze. He sends visions of the entire course of the Mortal Kombat timeline to himself in the past right before the tenth Mortal Kombat tournament (first game). This transfer of information to his former self causes a rift in time causing the Armageddon timeline to be erased and a new "reboot" timeline to be introduced, with a new outcome of Mortal Kombat history to be written. But this story leads to even worse unforeseen events. It ends with many of the main game characters dying at the hands of Queen Sindel and eventually Raiden accidentally kills Liu Kang in a fit of rage. But eventually the Elder Gods aid Raiden in killing Shao Kahn and saving Earthrealm. But as the scene goes on it is later revealed that this was all a plan by Lord Shinnok and Quan Chi.