Here is my view on how the story should be portrayed.

Prologue
After the defeat of the Deadly Alliance, earths warriors (sonya,jax,raiden,johnny cage,kai,kung lao,sub-zero and kitana) celebrated their victory at the temple of the order of light. All of a sudden the clouds turn purple and black. A portal opens and the Dragon King appears and says the following: "Earth's warriors I am your new master, bow before me!" Rayden uses his thunder to close the portal but all of a sudden his powers cease. "Your powers are futile for eternity!" "I have defeated the elder gods with the aid of your ally." The dragon king says while laughing. All of a sudden a deadly wind blows and Fujin appears. Earths warriors are shocked to see him aid the Dragon King. "Well if it isn't Raiden", says fujin. "How could it be?" Raiden replied. Fujin says the following in a dark voice. "Your a fool to aid the forces of light. While you have been defending earth from its previous threats, I have been making plans for deception!"

The Preemptive Strike
Fujin then hits raiden with a brutal wind that sends raiden into the air. Raiden crashes into the ground. "You see, even your god is no match for my power." Fujin says as he approaches earths warriors. "No!" "You're gonna pay!" Johnny Cage shouts. Cage then runs towards Fujin and attemps to do a flying shadow kick, but Fujin uses the power of wind and slams Johnny violently into the ground. Fujin then lifts Johnny into the air and Sonya attempts to aid Johnny, but Jax holds her back. "Witness my power!" Fujin shouts. Sonya pushes Jax back and runs toward Fujin screaming, but as she approaches Fujin, the Dragon King shoots an energy ball at Sonya, it pierces her body. Sonya turns around to look at her friends for one last time and she drops dead. Jax then falls to his knees. Fujin summons a dark whirlwind, the irresistable force grabs Johnnys frangible body and literally tears him apart. Earths warriors watched defenselessly as the Dragon King consumed the souls of Johnny Cage and Sonya. "In a matter of time, my undefeatable army will reign earthrealm and conquer it for eternity." The Dragon King said as he levitated Raidens humble body over him. The Dragon King and Fujin then vanish with Raiden. "We have to stop them!" Shouted Kung Lao. "But how?" "They have Raiden!" Said Jax. "There is still hope." Sub-Zero Mumbled. "Sub-Zero and I will travel back to outworld to stage an attack against the Dragon King." Kitana said. "We can recruit earths mightiest warriors and prepare earths defenses for a possible invasion." Kai said. "Fine." Said Kung Lao. Kitana and Sub-Zero travel to Outworld through the portal that the Dragon King used to enter earthrealm. Kai, Jax and Kung Lao watch as the portal closes behind them.

Enjoy