The Defenders of the Realm face a pack of invading cybers (seemingly Shao Kahn's basic footsoldiers) lead by Sektor and Cyrax. The situation takes a turn for the worse until Sub-Zero intervenes and assists the warriors in forcing the invaders back to Outworld. Sub-Zero tries to warn the warriors of the incoming threat from Scorpion, although Sonya Blade is hesitant to believe him due to the fact he betrayed his clan. Following Raiden's instructions, the warriors relunctanty return to base with Sub-Zero in company. Shortly afterwards, a group of Tarkatan warriors locate and invade the base, further raising Sonya's belief that Sub-Zero has betrayed them. After staving off the Tarkatan invaders outside, Sub-Zero and Nightwolf fight off the ones inside - Sub-Zero defeats their leader, Karbrac - and Sonya is finally convinced that the runaway Lin Kuei is on their side. Before apologies can be made, an alarm sounds, indicating Scorpion's approach.

In the mountains of Tibet an ancient tomb is hidden, with which one can gain access to other worlds. Scorpion aims at getting there in order to organize the army of dead warriors to invade the earth. To prevent this, Sub-Zero challenges Scorpion to a kombat, but Scorpion appears to be stronger than he. The next earth warrior that fights Scorpion was Liu Kang who manages to defeat the dead ninja and bring his plans for world domination to an end.

A new dangerous enemy of Earth, creatures of a strange reptilian race led by Reptile himself, appears before the earth warriors. During the attacks that followed the acid of one of the reptiles hits Jax's cybernatic hands. As a result of this an important microchip gets lost and his hands don't function anymore. Because of this Jax loses his self-confidence. Sonya returns to the place where battle was fought to find the microchip and help her friend. However, Reptile manages to kidnap Sonya. Because there are also other battles to be fought, the Earth Warriors decide to split up: the larger part of the team take off to a kombat with Sheeva's Shokan warriors, and Jax starts his search to find his partner, Sonya. In his desire to help Sonya, Jax forgets about his cyber-hands and defeats Reptile on his own. At the same time the rest of the warriors manage to win their battle too, with Raiden proving instrumental in their victory.

A strange energy emission in New Guinea leads the Earth Warriors to Rain, an old friend of Kitana. He informs them that Shao Kahn is seeking a powerful weapon hidden in a sacred temple. The Earth Warriors ready for battle before it's too late, only to discover later that Rain is a traitor and has kidnapped Kitana. Liu Kang confronts Rain in his castle, out of jealousy, but Kitana is the one who fights Rain. As the battle comes to a close, the castle starts to fall apart - Rain flees while Liu Kang and Kitana return to safety with Raiden's help.

Sub-Zero goes out to meet with his friend Smoke, who unexpectedly returns after being gone for many years. Sub-Zero and Smoke were best friends before Oniro, the leader of the Lin Kuei clan gave the order for automation of the Ninjas. Sub-Zero managed to escape this fate, but Smoke was captured and got the cybernetic augmentations. Now Sub-Zero wants to know if his old friend still has the soul of a man or if he became only a machine for murder. Smoke's orders are to annihilate Sub-Zero and the icy warrior is trapped. His friends come to help him and begin the battle with forces of Lin Kuei. Smoke's soul was still in his automated body and gets the upperhand, and fights with his friend Sub-Zero once again. They go after the Oniro, who possesses the ability to transform in animals, but the strong duo don't give up. They defeat their one-time leader and Smoke bids goodbye to Sub-Zero and disappears again, possibly until he finds himself again.

When Kano creates unnatural holes on Earth with the purpose to torment the Defenders they realise that the Black Dragon is back again. Nightwolf gets very worried after leading his fellow warriors to temporary portal rips that close before they arrive, as they deem all of these happenings are wrong readings of his computers. Encouraged by Raiden, he uses his magic force to find out where the black dragons are; it turns out their shelter is hidden under an Egyptian pyramid. When the Earth Warriors arrive there, they encounter and defeat the mummy-guards. Then the struggle with Kano begins, who had already lost an earlier fight with Sonya in the first Mortal Kombat tournament and loses this fight as well. Kano tells them that the pyramid is rigged with explosives, but the Earth Warriors escape the pyramid just in time to escape the explosion.

In a battle against Shokan warriors, Sonya acts with overconfidence. As a result, Stryker is seriously wounded. He decides to suspend Sonya because he feels she can't work as a team with the others. After being ordered to take Stryker back to the compound, with Nightwolf out to help fending off Sheeva's troops, they are attacked by a detachment of Shokan warriors. Learning a lesson on teamwork while battling the Shokan warriors she regains Stryker's confidence and is reinstated.

Quan Chi finds a magic crystal with which he is able to awaken all the evil in a human soul. Using it, the magician influences the Earth Warriors and makes them hate each other. The Earth is now out of any defence, and would be conquered by Quan Chi, if not for Nightwolf who escaped the crystal's influence. It is Nightwolf who destroys the evil crystal and ruins Quan Chi's black magic.

Shao Kahn resurrects Shang Tsung and entrusts him with a sphere that controls the elements of nature (fire, wind, water and earth). Shang Tsung is the most suitable person to possess the sphere, because the more malicious the master is, the stronger the magic sphere becomes. The old enemy of good organizes different natural disasters and weakens Raiden. The Earth Warriors are trapped, so nobody can help the God of Thunder. Thus, he is the one who has to decide the fate of the world. But good, even though it grew weak, is stronger than the evil even when strengthened with the forces of magic. Having defeated Shang Tsung, Raiden sends the sphere to the space. Strangely at the end of this episode, a mysterious figure runs into the portal to follow the sphere - the identity of this person is never fully revealed.

This episode begins with a battle between Kitana and the Amazon Leader. A guard arrives in time and arrests Amazon. Although the battle was interrupted, Kitana knows that it will continue some day. Many years ago the enemy of the princess returned. In the past, the Amazon managed to find one of the two Swords of Ilkan. When these swords are connected, it is possible to open portals to other worlds. To get to the second sword Amazon Leader takes Jax as a hostage. Kitana and Sonya have to go to planet Ilkan to save their friend. They defeat the gigantic guard and take the sword, but Kitana decides not to give the mortal arm to people with dark feelings. The unfinished battle continues and this time the princess wins. The swords of Ilkan are now in the hands of defenders of good.

Sonya and Sub-Zero go out to find out the plan of the Black Dragons. Suddenly they are attacked and Sonya was close to death but she was saved by a former member of Black Dragon - Kabal. Years ago Kabal was one of the best warriors in his clan, but Shao Kahn thought that he was too dangerous and ordered to destroy him. By a miracle Kabal survived in his fight with the hired killers, but his face was viciously scarred. He puts on his mask and begins a battle against Shao Kahn and Black Dragon. Kano and his servants make a Portal to lead the army of evil to other worlds. With the help of Kabal the earth defenders manage to crush these forces unleashed by Kano and destroy the Portal. The Earth Warriors offer Kabal the chance to join them but he chooses the way of a lone warrior. Sonya is notably moved by Kabal's story and is upset when he leaves.

Jax is tired of the endless battles and wants to leave. His friends try to dissuade him from this, but Jax insists on his decision. He leaves the squad and goes to the house of his dead grandfather. There he makes the acquaintance of a girl called Ruby. However, Ruby is one of Shao Kahn's agents. She tries to find out the location of Earth Warriors's base. Jax, who didn't expect any danger, now finds himself captured by Ermac's forces and is imprisoned in a cave under Shao Kahn's castle, where he was put for torture. Luckily, his friends know about these events and go out to help him. But the Earth Warriors are outnumbered by Shao Kahn's troops and are surrounded. It seems that their destruction is inevitable, but at this moment Ruby decides to help the Earth Warriors. She leads the Earth Warriors through a hidden exit. Jax realizes that a peaceful life is impossible while the Earth is exposed to danger from another realm and returns to the team.

The Defenders of the Realm prepare for the final battle with Shao Kahn's forces. Kitana brokers an agreement with Sheeva's Shokan Warriors, but she doesn't know that she is in fact the cruel Shang Tsung who transformed to look like Sheeva. Kitana and the rebellion forces break into Shao Kahn's castle and demand that Shao Kahn hands over his rule to the princess. Suddenly Shang Tsung appears with the warriors of the real Sheeva. The magician is also after the throne of Outworld. But Tsung forgets one thing; Sheeva and the Shokan also have enemies in Outworld. Raiden finds out Shang Tsung's plan and disrupts the fight. The god of thunder brings with him the worst enemy of Sheeva; Motaro, and the whole Centaur and Tarkatan army. The defenders escape through a portal as the Shokan and Centaurs do battle. The insurrection may have failed, but the realm of Earth has not fallen and Mortal Kombat continues.