Kung Lao has triumphed in the Mortal Kombat tournament, defeating Shang Tsung and saving Earth Realm. Now, he must train a new generation of warriors for the next tournament. Meanwhile, an exiled Shang Tsung attempts to thwart Lao's efforts with the aid of supernatural warriors such as Scorpion and Sub-Zero.
Reluctant warrior Kung Lao has defeated Shang Tsung in Mortal Kombat and become tournament champion. Following his victory, Rayden tells Kung Lao it is his duty now to train warriors for future tournaments. But will Kung Lao follow his destiny or marry the woman he loves?
Siro warns Jen that something is wrong with her new guard, Takeda. But he is unaware Shang Tsung sent Scorpion to possess Takeda and eliminate Kung Lao, who has been sentenced by the Baron to die. Rayden convinces Siro and Taja to help.
Kung Lao, Taja and Siro must stop Shang Tsung and Lin Kuei assassin, Sub-Zero, from acquiring a magic crystal.
After the mysterious death of a monk, Kung Lao learns Shang Tsung sent Vorpax to poison his water sack with an aging potion. But Taja and Siro have already drinked the rest of the potion and are beginning to grow older and older.
The Essence of Edenia, long thought destroyed, has been secretly moved to Earth Realm. Kung Lao meets Princess Kitana, who convinces him to save the last hope of the Edenian people.
Siro and Taja meet a seer named Kiri, who tells them of an underworld city with a shrine guarded by two powerful warriors. Kiri says they will grow stronger if they defeat these warriors, but she really hopes they will release Noob Saibot to kill Kung Lao.
The Black Dragon, an infamous underworld organization, have appeared in Zhu Zin. They claim ownership of the trading post and demand Kung Lao, Siro and Taja leave. While they resist the Black Dragon, a member named Jola makes a deal with Shang Tsung for power and revenge.
Taja is pulled into a portal and arrives in the Cobalt Mines, captured by Shang Tsung. Kung Lao and Siro have to save her, even if it means walking into a trap.
Quan Chi sends a trio of women to infect Kung Lao, Taja and Siro with a potion. The potion enlargens their flaws: Kung Lao's temper, Siro becomes a drunk and Taja is a thief again. With the three getting out of control, Rayden has to find a way to break this spell before it's too late.
Shang Tsung forms an unlikely alliance with Quan Chi to defeat Kung Lao. They lure Kung Lao into a realm with everything he could possibly want. But it's all an elaborate trap for Shang Tsung to capture him and leave the Earth Realm defenseless.
An old love from Siro's past, Hannah, turns up in Zhu Zin in search of his help. Hannah reveals she married Siro's estranged brother, Cassar, who has gone missing. Siro is reluctant to help until he learns Scorpion used magic to make Cassar one of his warriors.
Kung Lao is badly wounded in a fight with Rain. With him practically defenseless, Shao Kahn sends Mileena to masquerade as Princess Kitana and finish off the weakened Kung Lao.
A warrior named Tomas arrives, saying he wants to join Kung Lao in defending Earth Realm. All seems well until it looks like Tomas has murdered some barmaids. Has he? Or is there something bigger going on?
A traveling circus arrives in Zhu Zin with Qali among it. Kung Lao, Taja and Siro suspect something is wrong and they're right. The circus turns out to be a way for Quan Chi to raise an army.
Shao Kahn partners two bitter enemies, Sub-Zero and Scorpion, to destroy Kung Lao.
Empress Kreeya arrives on Earth Realm to build up an army. Her target: Outworld. Vorpax, revealed to be working for Kreeya, invites Kung Lao, Taja and Siro to join them.
Long ago, Master Cho was betrayed by Shang Tsung so he could fight for Shao Kahn. Now, Shang Tsung loose on Earth Realm, Master Cho intends to settle the score.
Kreeya has returned and is now teamed up with Reptile.
Shao Kahn enlists Quan Chi to find the missing Shang Tsung and return him to the Cobalt Mines.
Kung Lao is haunted by visions of Earth realm's annihilation. Meanwhile, Siro catches a thief in the trading post and it turns out to be Taja's old friend, Dion.
Shao Kahn continues his search for the traitor. Meanwhile, as Kreeya's forces are losing the war with Outworld, Vorpax seeks the help of the Earth Warriors to kill Kreeya.
Rayden meets in between realms with Shao Kahn, who says he will be defeated. Kung Lao, meanwhile, is looking for Rayden when he runs into Kitana. She warns Shao Kahn is planning to attack. Many of the other enemies of Earth Realm appear as well with plans of their own.