Armageddon took place because the Elder Gods felt that the kombatants were getting out of hand and could tear the realms asunder, right? So, the cause of Armageddon was the Elder Gods.
I think I know how Raiden prevented Armageddon.
I can't explain CSZ, but I can explain Johnny being saved.
Okay. Follow me on this trigger of events. Johnny was SUPPOSED to be killed by Motaro, but Raiden killed Motaro instead. In reaction, Shao Kahn gave Sindel insane power to kill the heroes. AND SHE DID.
NOW, Quan Chi has 10 souls (I'm not counting Liu Kang) under his control. Shao Kahn is defeated, and Shinnok is on the rise.
My Theory: The only way to prevent Armageddon is to kill the Elder Gods, whom started Armageddon themselves.
The main difference between the current story and the MK4 story from the past is:
-There are fewer heroes.
-Quan Chi has control over the 10 heroes.
-Liu Kang is no longer faithful to Raiden.
What difference does this make? Shinnok and Quan Chi now have the army to destroy the Elder Gods, in the 10 heroes. Not to mention, they could easily use Stryker to get aid from military from Earthrealm, Jax to get aid from Special Forces, and Kung Lao get aid from the Shaolin. Quan Chi has ten very powerful souls in his hands.
Raiden has put forth a chain of actions that will destroy the Elder Gods and himself. So my theory of the next game is:
Raiden, Johnny Cage, Sonya Blade, Kai, Fujin, Ermac (restored now that Shao Kahn is gone and is possibly King Jerrod), Cyrax (turns good much like MK4), Scorpion (in hopes to destroy Quan Chi), Noob (read Scorpion), and possibly Mileena for the sake of Outworld...
Shinnok, Quan Chi, Tanya, Rain (manipulating Edenia), and the 10 warriors.
-Shinnok would succeed in killing the Elder Gods.
-Raiden would be killed.
-Fujin would be killed.
-Ermac or some Deus Ex Machina of some sort could bring the dead heroes back.
-Scorpion and Noob team up to kill Quan Chi.
-The heroes destroy Shinnok.
-The heroes reunite, but must live on in a world without the Elder Gods or Raiden's guidance.
-Liu Kang is neutral to everything.