Johnny Cage, Kitana, Sonya, Jax, Kung Lao were killed by the deadly alliance
Jax killed Hsu Hao
Mavado killed Kano
Kabal killed Mavado
Frost killed herself when stealing Sub-Zero's medallion
Nitara went back to her world, and Cyrax is trapped in Earthrealm
Reptile becomes Onaga, Onaga uses his body
Shang Tsung and Quan Chi might have been killed by Raiden's explosion. I think they were because you see them in the prison revived. And I don't know what happened to Blaze, Mokap, Moloch, Drahmin.

Funny thing is that Shang Tsung got imprisoned in his own prison complex under his island fortress.

Anyway, Hsu hao is dead by Jax, Nitara and Cyrax are both thrown back to their homeworld, Frost is seemingly killed by the attempt to steal the amulet from Sub-zero, but there is a high percentage that shes only hibernating.

drahmin and Moloch wander around in Outworld aimlessly, becouse Drahmins ending could not have happened, since Quan Chi battles Shang Tsung at the end..and seemingly wins.

OK...

-Johnny Cage, Sonya, Jax, Kitana and Kung Lao: All died on the attack against the Deadly Alliance and were resurrected by Onaga. They now serve him.
-Kano- Killed by Mavado
-Reptile- Vessel for the Dragon King
-Shang Tsung and Quan Chi- Blown up by Raiden in the intro
-Cyrax- Probably stranded somewhere in Earthrealm
-Mavado- Killed by Kabal
-Drahmin and Moloch- Probably just wandering around somewhere, killing mortals
-Frost- Died when she grabbed Sub Zero's Dragon Medallion and was consumed by ice
-Hsu Hao- Killed by Jax
-Nitara- Back in her home realm, plotting
-Blaze- Back on the quest he was on before the Dragon King enslaved him
-Mokap- Don't know, don't care!
-Sareena (MK: TE)- Unknown. She may have gained sanctuary with the Lin Kuei, as her ending says
-Sektor (MK: TE)- Currently taking over Japan with his Tekunin Clan

There you go!

Well I dont really think Hsu Hao is dead. Because, before MK:Deception was released, we were told Jax's ending was canon. But then he was killed in the intro with the others, so his ending couldn't have happened. Hsu Hao is probably still alive.

Yes, but Jax's ending could have happened just before he was killed by the Deadly Alliance

And of course as MK:TE revelaed...Noob Killed Goro. Sorta.

I dont think they are killed. To me they fallen in the battle. Just are defeated.

Ermac's ending show some Deadly Alliance characters like they was controlled by Onaga powers. Maybe Onaga keep them locked in Dark Prison (not the background with every character of MK series).

But if you think that they are killed, well, Onaga has the power to raise the dead. Maybe he did it.

What happened to Raiden? He's a lot more... sinister-ish now. I have yet to defeat Onaga with him, so I dont know if that would clear it up. What happened to him in between MKDA and MKD? I know he lost the battle against Onaga, but it doesnt clear it up for me...

They did die. But Onaga resurrected them and brainwashed them to be loyal to him. Says it in Jade's bio.