I suspect Quan Chi teleported out of there before the palace blew. In the intro we see him start to run away before Raiden blows up.
He's probably hiding out, regaining his power and planning his next move.
But Shang Tsung wasn't so lucky. It's confirmed in Liu Kang and Kenshi's bios that Shang Tsung did not survive the blast.
I suppose it's possible he somehow survived the blast and lost all their souls in his weakened state, but Tsung surviving seems less likely than Quan Chi surviving.

Isnt Raiden Evil??????????????????
so yeh the dragon king might of resurected him!!
anyways...................i do remember something bout deceptions starter say that Tsung and Raiden Died it said nothing bout Quan Chi Dying!!!!!!!!!!!

Raiden's not evil. He's just pissed.

actually somewhere in the game it says that gods can never truly be killed only put in like a hibernation state until there physical bodys can reform as raidens did. also raiden isnt truly evil or good anymore. all he cares about now is saving earthrealm at all costs. so if someone fails in saving the earthrealm then he well destroy them for failing. hes doing the right thing the wrong way so to speak.

I remember watching the Quan Chi, Shang Tsung, and Raiden shooting their energy at Onaga. While Raiden was charging up his thunder bolt Quan Chi was the only one aware of what Raiden was doing. Quan Chi even yelled out "What are you doing?" as he looked over at Raiden.
I remember before the blast went off Quan Chi began to run away. Shang Tsung was not aware of what was going on and the blast hit him fully. I believe Shang Tsung is dead, but not Quan Chi.
I agree with the previous statement on Quan Chi. I too believe that Quan Chi is hiding in Outworld somewhere planning his next move. I think that Quan Chi would be injured due to the blast so we might not see any sign of him untill Mortal Kombat 7. I just hope that he is more level as a regular player than being the boss in the next game.

yea like subzilla said man...raiden is an imortal...you can kill his shell but his essence still remains...thats what he does to blown him self up...release his essence/soul from his body!...he can come right back!
heres what i think...Quan and Shang ARE DEAD! but but but! listen
when raiden blew him self up he released there essence as well...and it was merged with his! making him the DICK he is now lol! he will have to get rid of this and cast shang and quan OUT! ...or maybe havik will resurect them! seeing how he fights like both of them put together!!
i think they all three know each other....maybe quan and shang created havik....maybe he created them...but i know they will be back fear not...but i know im not alone when i say this...shang sucks with out his morph! :( but i understand the programing difficulties!!