"Much has changed since the last Mortal Kombat Tournament. Dark forces of Out World have begun invading the Earth Realm. These attacks are seriously weakening Earth's dimensional fabric. Enabling not only Outworlders to enter the Earth Realm, but warriors from other domains as well. Only the most extraordinary warriors could possibly meet this challenge." - These are the words of Rayden.
On the anniversary of her father's death, princess Kitana has planned a rebellion against Shao Kahn. If it succeeds, Kitana will reclaim the throne of Outworld - leaving Liu Kang and the other combatants.
Feeling overwhelmed and the need for a real life, Jax considers quitting the team. While he is away, the emperor Shao Kahn attacks the headquarters.
Kitana is confronted with her past when a handsome young ninja from Outworld seeks her out, which stirs jealousy in Liu Kang. However, the ninja proves to be working for Shao Kahn and abducts the princess. It's up to Liu Kang to save her.
Quan Chi a free-roaming sorcerer versed in the dark arts, uses an ancient gem to turn our heroes against one another.
Sub-Zero's nemesis, Scorpion, is traveling from real to realm unearthing an army of evil dead. Sub-Zero's hatred for Scorpion gives the ghost ninja the advantage. It is up to Liu Kang to overcome his self-doubt and face the incredibly powerful Scorpion alone.
Nightwolf repeatedly sends the combatants to "rips" that don't appear to exist. They begin to think his computer skills are shot. Finally, Nightwolf discovers that it's a clever ruse which Kano is behind, triggering intense feelings in Sonya who thought the thug was dead - feelings that she failed her old partner.
With the help of the shadow priests, the emperor Shao Kahn succeeds in resurrecting Shang Tsung. The emperor then dispatches Shang to Earthrealm, armed with the most powerful weapon of them all - the Warrior King's orb.
Sonya is feeling overwhelmed by the endless fighting and the lack of any other females to relate to. She tries to get close to the illusive Kitana, who is faced with a painful part of her past when they travel to a realm ruled by a ruthless Amazon-like warrior.
While tracking Kano and the Black Dragon organization, the team discover they have a phantom ally, who turns out to be Kabal. Having been disfigured by Shao Kahn, Kabal is considered a freak. Sonya overcomes her own revulsion, then helps the others see past the ugliness to the man inside.
While the mortal combatants are battling Cyrax and Sektor, they are joined by Sub-Zero. This triggers memories and self doubt in Liu Kang, and mistrust for the ice ninja in Sonya and the others. When headquarters is attacked, Sub-Zero must prove where his loyalties really fall.
During an intense battle against Komodai, a reptilian ninja, Jax suffers and injury to his bionic arms. A rare chip is lost in action. His unique arms cannot be repaired before the combatants are forced into action again. Jax is facing his worst fear - that he is nothing without the strength of his bionic arms.
Sub-Zero has a run-in with his old friend Smoke, who is now programmed to destroy the ice ninja. He must convince Smoke the that he still has a soul before the cyber assassin takes him out.
Sonya's recklessness injures Stryker, and the team vote to suspend her. As they struggle to drive back an assault on Earthrealm, Sonya and the injured Stryker are the only ones left to defend the headquarters against an invasion by Shokan warriors.