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.

Bo Rai Cho: trainer of martial arts; taught Liu Kang his fighting skills and passed them to Kung Lao.

Johnny Cage: aided Raiden in stopping the Deadly Alliance. Killed in battle with Quan Chi and Shang Tsung.

Kano: pledged his alliance to Shang Tsung and Quan Chi, made a general in Shang Tsung's army and ordered to kill anyone who interferes. Killed fighting Mavado.

Kenshi: Wandered the Outworld to face Shang Tsung. Severely injured fighting Mavado, but saved by Sub-Zero.

Kung Lao: aided Raiden in stopping the Deadly Alliance. Killed in battle with Quan Chi and Shang Tsung.

Li Mei: promised her people would be freed if she won a fighting tournament. She won, but her efforts were in vain; her soul was transfered into a Dragon Soldier's body, but was saved by Bo Rai Cho.

Mavado: Red Dragon gang member, hired by Quan Chi to kill anyone in his path. Severely injured Kenshi and murdered Kano in battle. Newest plan was to destroy the Lin Kuei.

Quan Chi: one-half the Deadly Alliance. He killed Shao Kahn and Liu Kang with his partner Shang Tsung. They planned to conquer all realms unless defeated in combat. The heroes were all killed, and even Raiden could not win. They then fought each other, and Quan Chi came out victorious...until the arrival of Onaga, the Dragon King...

Scorpion: stayed neutral in the fight, entered Shang Tsung's fortress and simultaneously fought Moloch and Drahmin. He lost and was thrown into Shang Tsung's soulnado.

Shang Tsung: one-half the Deadly Alliance. He killed Shao Kahn and Liu Kang with his partner Quan Chi. They planned to conquer all realms unless defeated in combat. The heroes were all killed, and even Raiden could not win. They then fought each other, and Shang Tsung was defeated...until the arrival of Onaga, the Dragon King...

Sonya: aided Raiden in stopping the Deadly Alliance. Killed in battle with Quan Chi and Shang Tsung.

Sub-Zero: aided Raiden in stopping the Deadly Alliance. He and Frost were seperated from the team and lost in Outworld when Frost revealed her treachery. When her betrayal cost Frost her life, Sub-Zero was forced to bury her dead body.

Moloch: An oni demon alongside his partner Drahmin, he was hired by Shang Tsung in an act of safe measures against his new partner. After a two-on-one fight, they threw Scorpion into Shang Tsung's soulnado.

Cyrax: stranded in Outworld due to the seperately combined efforts of Mavado and Nitara. Cyrax now had little choice but to aid Nitara in her search for a magical orb. Once she got what she wanted, she sent Cyrax back home back home to Earth.

Drahmin: An oni demon alongside his partner Moloch, he was hired by Shang Tsung in an act of safe measures against his new partner. After a two-on-one fight, they threw Scorpion into Shang Tsung's soulnado.

Frost: aided Raiden in stopping the Deadly Alliance. She and Sub-Zero were seperated from the team and lost in Outworld when Frost revealed her treachery. She froze her master to the wall, and stole his Dragon Medallion. The medallion was too powerful for her, and she perished.

Hsu Hao: responsible for the Outworld Investigation Agency's destruction. Instructed by Mavado to inform Quan Chi about his partner. As he ran, he was ambushed by Jax, who proceeded to rip his cybernetic heart out.

Jax: aided Raiden in stopping the Deadly Alliance. He killed Hsu Hao by ripping out his heart. Killed in battle with Quan Chi and Shang Tsung.

Kitana: aided Raiden in stopping the Deadly Alliance. She mourned the loss of Goro and only wished Liu Kang would have accepted her offer to be her king. Killed in battle with Quan Chi and Shang Tsung.

Nitara: a vampiress who manipulated Cyrax and Reptile to do her dirty work.

Raiden: Religuished his status as Elder God to lead the heroes to victory. It didn't go as he planned...

Reptile: conned by Nitara to damage Cyrax, and feeling bad about not being there to save his master. Later, inside the volcano, he found the Dragon Egg, which, when the light lanced into his body...Reptile became the vessel for Onaga, the Dragon King.

Canon (in-game) endings:
Bo Rai Cho: ending happened because he moved from Outworld to Earthrealm.
Li Mei: ending happened because she was double-crossed, but saved by Bo Rai Cho.
Mavado: ending happened because he killed Kano and plotted to destroy the Lin Kuei.
Scorpion: ending happened because he lost to Moloch and Drahmin.
Cyrax: ending happened because he successfully aided Nitara.
Frost: ending happened because she tried to betray Sub-Zero and died for it.
Hsu Hao: ending happened because it ties into Jax's ending.
Jax: ending happened because he killed Hsu Hao.
Kitana: ending happened because she mourned having lost Goro and Liu Kang.
Nitara: ending happened because she used the crystal ball to return to her home realm.
Reptile: ending happened because he became a vessel for the Dragon King.

Non-canon (in-game) endings:
Johnny Cage: ending didn't happen because he was killed by the Deadly Alliance.
Kano: ending didn't happen because he was killed fighting Mavado.
Kenshi: ending didn't happen because he was injured fighting Mavado, but saved by Sub-Zero.
Kung Lao: ending didn't happen because he was killed by the Deadly Alliance.
Quan Chi: ending didn't happen because he turned on Shang Tsung after beating Raiden and Kano is dead at that point.
Shang Tsung: ending didn't happen because he turned on Quan Chi after beating Raiden.
Sonya: ending didn't happen because she was killed by the Deadly Alliance.
Sub-Zero: ending didn't happen because he was still in Outworld at the time.
Drahmin: ending didn't happen because it interferes with the MK:D plot.
Raiden: ending didn't happen because he lost to the Deadly Alliance.

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