Picking up from where the last installment concluded, the Earthrealm warriors—Liu Kang, Sonya Blade, Johnny Cage, Princess Kitana, and Rayden—return to the Temple of Light following Liu Kang's victory over Shang Tsung in Mortal Kombat and his thwarting of the Emperor's plot to seize Earthrealm. Unfortunately, the celebrations are brief, as a portal to Outworld opens above the temple, unleashing a formidable army led by Shao Kahn and his generals—Ermac, Shiva, Motaro, and the newly resurrected Queen Sindel. They ominously declare that in just six days, the realms will merge, allowing Kahn to claim both.
Determined to protect their realm, Rayden challenges Kahn to a duel. However, during the intense confrontation, Kahn gains the upper hand and brutally murders Johnny Cage. With their forces diminished, the Earthrealm fighters retreat as the temple succumbs to Kahn's might. Rayden reveals that Kahn has discovered a method of invasion unbeknownst to the Elder Gods. The fighters strategize to bolster their ranks and prepare for an all-out assault against Kahn's forces before the union of realms occurs.
Using a network of subterranean tunnels that draw heat from the planet's core, the team splits up to rally support. In a desolate military research facility, Sonya encounters fellow special forces agent Jackson "Jax" Briggs, who has undergone a transformation with bionic muscle enhancers. As Sonya explains Kahn's imminent invasion, they are ambushed by one of Kahn's extermination squads led by the Lin Kuei assassin-turned-cyborg Cyrax. During the chaotic battle, Sonya ingeniously ignites Cyrax, incinerating him, before the two agents narrowly escape as the facility erupts into a blaze.
Meanwhile, Liu Kang and Princess Kitana embark on a quest to find the enigmatic shaman warrior Nightwolf. As they navigate through crumbling ruins, they encounter another Lin Kuei cyborg, the ethereal ninja Smoke. Though Smoke proves to be a challenging foe, they are unexpectedly aided by Sub-Zero. Revealing that he is the younger brother of the original Sub-Zero, this ally expresses his intention to assist the Earthrealm fighters.
After Sub-Zero constructs an ice bridge to replace the one destroyed during their battle, they are ambushed by Scorpion, who kidnaps Kitana and teleports to Kahn's stronghold. Liu Kang, relentless in his pursuit of both Nightwolf and Kitana, pushes onward. In his quest, Rayden seeks insights from the Elder Gods regarding Kahn's clandestine invasion. The Elder Gods inform him that only the reunification of Kitana with her resurrected mother, Sindel, can thwart Kahn's ambitions.
During his wanderings, Liu Kang finally meets Nightwolf, who instructs him that to conquer Shao Kahn, he must master the art of Animality through a series of rigorous tests. The challenges include one testing his self-worth and another involving the warrior Jade, who attempts to seduce Liu Kang but ultimately joins him in rescuing Kitana. Together, they make their way to the Elder Gods' temple to reunite with Rayden and their comrades.
After a skirmish between Jax, Sonya, and the mysterious assassin Mileena, who fails to defeat them, the Earthrealm heroes gather at the Elder Gods' temple where they encounter Rayden, now a mortal who sacrificed his divinity to fight alongside them. However, their reunion is abruptly interrupted as Kahn and his army devastate the temple.
Traveling to Outworld, Liu Kang aims to rescue Kitana while the others strive to capture Sindel to break Kahn's control over her. Liu discovers Kitana imprisoned and engages in combat with Baraka, ultimately defeating him and quickly dispatching Shiva with the falling cage. Though the group confronts Sindel, she manages to escape alongside Jade, who is later revealed to be a traitor working for Kahn before meeting her demise for her failure.
Amidst the unfolding chaos, Rayden reveals a shocking truth: he and Kahn are brothers, sons of the disgraced former Elder God Shinnok. With their original plan to free Sindel's soul no longer viable, the group prepares for one final confrontation against Kahn and his generals. In a powerful clash, Shinnok demands Rayden abandon Earthrealm, but Rayden steadfastly refuses, leading to his death at Kahn's hands. However, the Earthrealm fighters, including Jax, Sonya, and Kitana, emerge victorious in the ensuing battle.
In a climactic showdown, Liu Kang battles Shao Kahn, ultimately embracing his Animality to transform into a fierce dragon. Kahn, however, reveals his own Animality as a multi-headed serpent. In a struggle for dominance, the Elder Gods intervene, stating that the fate of Earthrealm will once again be determined through Mortal Kombat.
In their final conflict, Liu defeats Kahn, leading to the Elder Gods banishing Shinnok to the Netherrealm and resurrecting Rayden, granting him Elder God status. With the merger averted, Sindel is freed from Kahn's grasp and reunited with her daughter. With the world now safe, Rayden takes on his new responsibilities as an Elder God while advising the Earthrealm fighters to continue their battle for righteousness and to watch over one another.
