The story begins after the events of Mortal Kombat: Armageddon, where almost all fighters are

dead, leaving only Raiden and Shao Kahn. Defeated and about to be delt the final blow, Raiden
uses his last attempt to cast a spell on his amulet, now shattered, to contact his past self and quote
"He Must Win!" before he is killed.

During the events of the first game's tournament, hosted by Shang Tsung, the Raiden from that
era possesses visions of the events from the future, he notices his amulet has cracked, signaling
troubling times ahead. Across the tournament's battles, Raiden comes to the conclusion that Liu
Kang is to win the tournament and save Earthrealm. He urges him to fight Shang Tsung. He does
so and is victorious, however, Raiden's amulet cracks further, a sign that future events remain
unchanged. Disappointed with Outworld's defeat, Shao Kahn orders Shang Tsung's execution,
but relents after being given the proposal of holding the second tournament in Outworld. During
the events of the tournament, due to Raiden's assistance of Smoke, whom was to be subjected to
cybernetic transformation as per Lin Kuei orders, Sub-Zero instead undergoes the procedure,
inadvertently altering the timeline. Raiden attempts to substitute Kung Lao as the champion of
the new tournament. Kung Lao, however, is killed by Shao Kahn after defeating Kintaro, leaving
Liu Kang to be champion once again.

Despite Liu Kang's fatal victory over Shao Kahn, Kahn launches an invasion of Earth despite
warnings by the Elder Gods that by merging Outworld and Earthrealm, he will earn their wrath.
Nightwolf halts Quan Chi's ritual. However, the interference causes Shao Kahn's forces to assault
the headquarters of the Earthrealm warriors, as Kabal, Stryker, Cyber Sub Zero, Jax, Smoke, and
Jade are all killed and Johnny and Sonya injured by Sindel. Kitana unsuccessfully pleads her
mother, who comments that she is no longer her mother, and fatally wounds Kitana. Nightwolf,
in a desperate attempt kill Sindel, uses all of his remaining energy to destroy both himself and
the empress. As Raiden and Liu Kang return from an unsuccessful consult with the Elder Gods
was shocked of the event that took place. Liu Kang, upon seeing Kitana and all his allies dead,
becomes angry, believing Raiden to be insane with his visions.

During an attempt to ally with Quan Chi in order to stop Khan's invasion, Raiden realizes that
Shao Kahn is the one meant to win by merging the realms and meet with the monk about this
news. However, Liu Kang has already deemed Raiden insane as his efforts to change the past.
They fight, with Liu Kang threatening to kill him if he insists on interfering. Raiden
inadvertently kills Liu Kang instead just as Kang is about to intercept Shao Kahn. Overwhelmed
with grief and guilt over the loss of his friend as well as countless others, Raiden remorsefully
surrenders to Shao Kahn voluntarily. The Elder Gods intervene, and grant him the power
necessary to kill Kahn, freeing Earthrealm. Raiden vows to rebuild Earthrealm and tend to the
injured with Cage and Sonya.

In the end, Quan Chi is seen meeting with Shinnok. The two discuss using Earthrealm's
vulnerability in making the Netherrealm the dominating force in the universe.