The story of Mortal Kombat 11

Following Shinnok's defeat at the hands of Cassie Cage in Mortal Kombat X, a now-corrupted Raiden plans to protect Earthrealm by destroying all its enemies any way he can. Raiden incapacitates Shinnok by decapitation, which triggers Kronika, Shinnok's mother and keeper of time, to rewrite history in order to stop Raiden's interference. A Special Forces strike team led by Sonya Blade, Cassie, and Jacqui Briggs assaults the main cathedral in the Netherrealm, with Raiden providing a diversion to aid them. The team succeeds in destroying the base at the cost of Sonya's life. Kronika creates an alliance with Liu Kang and Kitana before causing temporal anomalies.

Kotal Kahn, the current emperor of Outworld, attempts to execute the Kollector, but is interrupted by Kronika. Shao Kahn, Skarlet, Baraka, and younger versions of Kano, Erron Black, Jade, Raiden, Kitana, Liu Kang, Johnny Cage, Sonya, Jax, Scorpion, and Kung Lao appear from an alternate timeline, while also causing Dark Raiden to be erased from existence due to the laws of time affecting him differently due to his immortal status, leaving Shinnok's amulet behind. The battle in Kotal's arena ends when D'Vorah transports Baraka, Skarlet, Black, Shao Kahn, and Kano to her hive, recruiting them into Kronika's fold.

Liu Kang, Kung Lao, and Raiden show up at the base after forging an alliance with Kotal Kahn. They learn that there is an energy signal under the Wu Shi Academy. Liu Kang and Kung Lao's investigation leads to a battle with Kronika's subordinate Geras and their Revenant counterparts, and ends with Geras getting away with powerful energy capsules containing Earthrealm's life force.

The special forces learn that Sektor is making a cyber army for Kronika. Sub-Zero and Hanzo Hasashi are sent there. With the aid of Cyrax, they shut down the cyber Lin Kuei, forcing Geras and both versions of Kano to revive Sektor and rebuild the cybernetic army. Raiden tries to consult with the Elder Gods. They refuse to help, but Cetrion, Kronika's daughter and an Elder Goddess, gives him ways to defeat her. Kronika recruits the present-day Jax to her side by tricking him into believing it was for the best to protect his daughter. Kotal Kahn and Jade go to a Tarkatan camp in order to turn them away from Shao Kahn, but Kotal's brutality and hatred towards the Tarkatans cause Jade to battle him, resulting in his defeat, before Shao Khan appears and captures them all.

The Special Forces base is destroyed by the Black Dragon and the cyber Lin Kuei, with the younger versions of Johnny Cage and Sonya captured in the process and Sektor being killed. Cassie leads a strike team to save her parents, where Sonya kills the younger version of Kano to erase his present-self from existence. Meanwhile, Kitana, Liu Kang, and Kung Lao battle Baraka in order to secure an alliance with him and Sheeva. With their aid, Kitana successfully kills Shao Kahn, uniting the Outworld factions and inheriting the throne from Kotal.

Raiden sends Jax and Jacqui to get the crown of souls from Shang Tsung's Island, but the pair are thwarted by Cetrion and present-day Jax. Hasashi is tasked with getting Kharon, the person who sends the unfortunate souls to the Netherrealm, to join their side so they can defeat Kronika. Hasashi fights his younger self, and persuades him to join his side. Right after the younger version agrees, D'Vorah poisons Hanzo. As he is dying, he tells Scorpion to get Kharon. Scorpion returns to the Fire Garden and is attacked by Raiden, due to Raiden's mistrust of the former after Scorpion betrayed Raiden after killing the original Sub-Zero years earlier. Raiden resorts to using Shinnok's amulet, resulting in Shinnok's influence beginning to corrupt Raiden once again, and Raiden engages in battle against Liu Kang. After Liu Kang repeats the exact same words from the battle where Raiden accidentally killed Liu Kang in the past, Raiden comes to his senses after realizing that his battles with Liu Kang in different timelines were a part of Kronika's machinations. Anticipating Raiden's realization, Kronika explains that her pitting Raiden against Liu Kang was due to their combined powers threatening her plans, and subsequently kidnaps Liu Kang. With Kharon recruited, Raiden, Scorpion, Sub-Zero, Cassie, Jacqui, Kitana, Sheeva, Jade, and Baraka lead a joint Earthrealm/Outworld task force to assault Kronika's keep. Geras is dropped in the bottomless sea of blood, Frost is defeated and shut down, disabling the Cyber Lin-Kuei, and the older Jax defects to the heroes' side.

Kronika sends Revenant Liu Kang to attack Raiden after absorbing the power from his past-self. After defeating the Revenant Liu Kang, Raiden merges with him, and becomes Fire God Liu Kang, and Liu Kang acquires the memories and knowledge of Kronika's plan through his Revenant-self. The heroes breach the Keep, only for Kronika to restore history to its beginning, except for Fire God Liu Kang due to his god-like status, and subsequently defeats Cetrion before engaging in battle against Kronika.

Depending on the outcome of the battle, the story ends in three different ways:

• If Liu Kang successfully defeats Kronika in two straight rounds without losing once, Liu Kang manages to reunite with Kitana, and both make vows to create a new and better timeline and undo the mistakes made by Kronika.

• If Liu Kang successfully defeats Kronika, but while also losing one round to her, Liu Kang is unable to bring Kitana back due to Kronika reverting history way too much, and instead, a now-mortal Raiden offers to become Liu Kang's advisor for as long as his lifetime lasts and the two begin to create a new timeline.

• If Liu Kang is defeated by Kronika, Kronika decapitates Liu Kang and announces the beginning of the New Era, although this proves to be a non-canon ending as the game has the player restart the battle.