The Plot

From Wikipedia.com:

Several years after the defeat of Shao KahnShinnok attacks Earthrealm with his army of Netherrealm forces, including the Earthrealm warriors who were killed during Kahn's invasion and are now resurrected as revenants underQuan Chi's control. After fighting their fallen comrades, a strike team led by Johnny CageSonya Blade, and Kenshi open a portal to Raiden's Sky Temple and head to the Jinsei Chamber, the source of Earthrealm's life force, where Raiden and Fujin are battling Shinnok and his Netherrealm forces. During the fight near the Jinsei, they distract Shinnok long enough for Raiden to steal Shinnok's amulet and imprison him inside it, but Quan Chi manages to escape. Johnny and Sonya track him to his lair in the Netherrealm and defeat him, successfully restoring ScorpionSub-Zero, and Jax to human form, though Quan Chi escapes again. In the years that follow, Johnny and Sonya marry and have a daughter, Cassie, but later divorce. Scorpion reinstates his Shirai Ryu clan, while Sub-Zero becomes the new Grandmaster of the Lin Kuei after killing Sektor.

Twenty years after Shinnok's defeat, Johnny Cage assembles a team of fighters composed of Cassie, Jax's daughter Jacqui, Kenshi's son Takeda, and Kung Lao's cousin Kung Jin. After undergoing a training exercise with Sub-Zero, they are deployed to Outworld to resolve a civil war between former empress Mileena, who has obtained Shinnok's amulet, and Outworld's current emperor Kotal Kahn, with whom Earthrealm has a peace treaty with. On Earthrealm, Sonya captures Kano and forces him to reveal where Mileena is keeping the amulet. Armed with this information, Cassie's team aids Kotal in recovering Shinnok's amulet and capturing Mileena. After executing Mileena, Kotal decides to keep the amulet in Outworld's hands, and takes Cassie and her friends hostage to prevent Raiden from retaliating. However, Kotal's second-in-command D'Vorah, who is revealed as a double agent for Quan Chi, steals the amulet. Cassie and her team escape captivity, and inform Sonya of D'Vorah's intentions.

Jax and Kenshi, aided by Sareena, lead an assault on the Netherrealm and manage to capture a weakened Quan Chi, who is brought back to Earthrealm and held at a refugee camp. However, Scorpion, having learned from Sub-Zero the truth of Quan Chi's involvement in the deaths of his family and clan, infiltrates the refugee camp with the intent of assassinating Quan Chi, defeating Kenshi, Johnny and Sonya in the process. As Scorpion prepares to kill Quan Chi, D'Vorah arrives with the amulet. Quan Chi manages to finish a spell moments before being beheaded by Scorpion, releasing Shinnok from captivity. Weakened by the Shirai Ryu's previous attack, Johnny is taken prisoner by Shinnok and D'Vorah. With the aid of Quan Chi's revenants, Shinnok and D'Vorah assault the Sky Temple, where they subdue Raiden. Shinnok then enters the Jinsei and corrupts it, transforming himself into an immensely powerful demon in the process.

Cassie's team pursues Shinnok, only to be intercepted by Kotal Kahn and his army. Although Cassie's team tell him about D'Vorah's allegiance to Shinnok, Kotal decides to kill them anyway, hoping to appease Shinnok and buy time to bolster Outworld's defenses. Sub-Zero and his Lin Kuei comrades appear just in time to repel the Outworld forces. At the Sky Temple, Jacqui and Takeda occupy the revenants, while Cassie and Jin enter the Jinsei chamber. There, Cassie defeats D'Vorah and Shinnok. A grievously-wounded Raiden then purifies the Jinsei, stripping Shinnok of his powers and forcing the revenants to withdraw. Sonya and her soldiers arrive, and the Cage family reunites.

Sometime later, the revenants Liu Kang and Kitana are revealed to have assumed leadership of the Netherrealm, but Raiden, hinted to have been corrupted in the process of purifying the Jinsei, warns them they will face "fates worse than death" if they threaten Earthrealm. As a final warning, he presents them with Shinnok's severed, yet still living head.