After defeating Kronika and Shang Tsung, Liu Kang, the God of Fire, uses Kronika’s Hourglass to recreate the universe before relinquishing control to Geras, becoming the protector of Earthrealm. Over time, he forms a fragile alliance with Outworld under the auspices of continuing the Mortal Kombat 1 Torrent tournaments. In the present, Liu Kang recruits fighters Kung Lao and Raiden, struggling actor Johnny Cage and former Yakuza member Kenshi Takahashi to compete in the latest tournament, with Raiden ultimately being chosen as Earthrealm’s champion and winning the tournament. Geras finds Liu Kang and informs him that Shang Tsung has returned with the help of a mysterious benefactor named “Damashi” and is acting as an advisor to Outworld’s Empress Sindel.
They travel to the wastelands of Outworld, where they encounter the Tarkatans, victims of the Tarkat virus, and witness Shang Tsung extracting bone marrow from the leader of the Tarkatans, Baraka. The Earthrealm fighters intervene, though Shang Tsung escapes to his laboratory. With Baraka’s help, the group locates the laboratory and stops Shang Tsung from apparently infecting Outworld’s princess Mileena with the Tarkat virus. However, Mileena attacks them, blinding Kenshi before Shang Tsung injects her with a serum to control her Tarkat symptoms. Her sister, Kitana, and General Shao arrive to capture the Earthrealm fighters. Shang Tsung tricks them before reuniting with his ally, Quan Chi.
The Earthrealm fighters are taken to the Pits of Flesh but escape with the help of Reptile and encounter Ashrah, who reveals that Quan Chi is building devices capable of stealing souls on a massive scale. Although Quan Chi uses several souls to create Ermac, the group defeats them and destroys one of the soul stealers before all but Baraka returns to Earthrealm. Liu Kang orders the Lin Kuei warriors Sub-Zero, Scorpion, and Smoke to destroy the soul stealers and capture Shang Tsung, but they are captured and Shang Tsung convinces Sub-Zero to join him, promising access to the Dragon Army of the Dead- alive.
