Basically, what happens to all the characters...

On this thread, I will try to briefly summarize the characters' individual fates in this game. I will do one for the sequels in the future.

Kai: helped defend Earthrealm from Quan Chi and Shinnok.

Raiden: mentored the heroes on their path to victory, and became an Elder God.

Shinnok: led his army of darkness to become the ruler of all reality. He was destroyed in combat by Liu Kang.

Liu Kang: defended the Earthrealm once again; he turned down Kitana's offer to rule Edenia as her king.

Reptile: made a general in Shinnok's army of darkness, served Shinnok under the promise that he would be returned to his own homeworld and save it from Shao Kahn's destruction. It never happened because Shinnok lost.

Scorpion: manipulated by Quan Chi to kill Sub-Zero under promise he would be returned to life. Before Sub-Zero fell unconscious, he told Scorpion his family's true killer still ran free. Quan Chi appeared and revealed himself, and prepared to return Scorpion to the Netherrealm. Quickly, Scorpion rushed the sorcerer, transporting him there as well.

Jax: helped defend Earthrealm from Quan Chi and Shinnok, rescued Cyrax from the desert.

Reiko: general in Shinnok's army. He was ultimately defeated in combat.

Johnny Cage: helped defend Earthrealm from Quan Chi and Shinnok.

Jarek: temporarily put his differences with Sonya and Jax aside to help fight Shinnok. After Shinnok's defeat, he rushed Sonya on a mountain top and missed, falling right off.

Tanya: secretly a Shadow Priest, she 'accidently' permitted Quan Chi and Shinnok into Edenia. At one point, the heroes likely discovered her ruse.

Fujin: the God of wind, he was one of the few remaining Earthrealm gods in action. On proving himself in battle, he took over Raiden's spot as protector of Earthrealm.

Sub-Zero: Still on the run from Cyrax and Sektor, with still attempting to stop Shinnok from making life hard for everyone. He was defeated by Scorpion, who finally revealed the truth about the true killer of his clan and family.

Quan Chi: acting as if loyal to Shinnok, Quan Chi had made a duplicate of Shinnok's evil amulet and handed over the fake to the fallen god. He ultimately spilled the beans to Scorpion and was transported to the Netherrealm.

Sonya: temporarily put her differences with Jarek, the last (known) member of the Black Dragon Gang, aside. After Shinnok's defeat, she dodged Jarek's attack and was also still the witness of Jarek (presumably) falling to his demise.

Cyrax: still after Sub-Zero but saved from the desert by Jax, he regained his will thanks to the Special Forces and became a Special Forces agent.

Mileena: now serving Shinnok, she plotted to (eventually) kill Shinnok herself to gain ultimate power. Attacked her 'sister' in the throne room but fell victim to a trap; she fell to her supposed death.

Kitana: helped wrest control of Edenia from Quan Chi and Shinnok. She once again murdered Mileena, made peace with Goro and thanked Liu Kang for his help; but he turned down her offer to rule Edenia at her side.

Kung Lao: helped defend Earthrealm from Quan Chi and Shinnok; settled his feud with Goro.

Baraka: sided with Quan Chi, waiting for an opportunity to kill Shinnok and rule along side Quan Chi. He never got the chance because Shinnok lost.

Noob Saibot: never truly given a story; highly possible he aided Shinnok.

Sektor: continued chasing Sub-Zero while keeping an eye on Cyrax. Chances are, he didn't get much done.

Canon (in-game) endings:
Raiden: ending happened because he went on to become an Elder God (for a little bit, anyway).
Liu Kang: ending happened because he won the tournament.
Scorpion: ending happened because it is a key factor in the MK:DA plot.
Johnny Cage: ending happened, but it's not important to the story.
Fujin: ending happened because he took Raiden's place as protector of Earthrealm.
Sonya: ending happened because she is alive in MK:DA and Jarek is for now considered dead.
Cyrax: ending happened because he regains his will and joins the Special Forces unit for MK:DA.
Kitana: ending happened because she defeated Mileena (again).
Kung Lao: ending happened because he and Goro officially ended their feud.

Non-canon (in-game) endings:
Kai: ending didn't happen because Raiden still has his lightning staff in MK:DA.
Shinnok: ending didn't happen because he was murdered.
Reptile: ending didn't happen because he's still alive and Shinnok is dead in MK:DA.
Jax: ending didn't happen because Sonya is still alive in MK:DA.
Jarek: ending didn't happen because Sonya is still alive in MK:DA.
Tanya: ending didn't happen because Shinnok is dead and Liu Kang lives until the introduction to MK:DA.
Sub-Zero: ending didn't happen because Quan Chi is still alive in MK:DA and his ending interferes with the MK:DA plot.
Quan Chi: ending itself didn't happen, but it explained how Shinnok was capable of being murdered.
Mileena: ending didn't happen because Kitana is still alive in MK:DA.
Baraka: ending didn't happen because Shinnok lost, he is still alive in MK:D and Quan Chi is alive until the end of MK:DA/start of MK:D.
Sektor: ending didn't happen because Sonya, Jax and Cyrax are all alive in MK:DA.

Unknown (in-game) endings:
Reiko: unknown.
Noob Saibot: unknown.

Kudos to Gavok's Mortal Kombat Canon Plot Guide
http://db.gamefaqs.com/coinop/arcade/file/mortal_kombat_plot.txt