This is only the end of the beginning... The last chapter of SF vs MK.
-Watch all three along with the prequel.
In the very end, It was all a plan that Shang Tsung made. He wanted warriors to fight off each other so that he can keep the souls of the dead and keep his run in immortality. He killed Gill a long time ago and the Gill seen here was nothing but a creation of Shang Tsung. He hates Kahn for betraying him in past events which is why he didnt protect him as he did in the last Round. He poisoned the mind of two universes to lead to Armageddon and his plan was a success. It was all well put. Raiden returns but with one specific purpose. He must be the protector of Earthrealm and mankind should not be trusted due to how they endangered Earth Realm. He will not hesitate to kill those who endanger Earthrealm. This new resurrected Raiden seems darker then before and only having the memory of defending Earth, alone.
The whole purpose of the apacolypse was caused by having, two universes filled with powerful warriors. Due to the selfishness of warriors they begun war with each other. Every realm slowly begins to get tainted and die,due to the increase in power of every individual battalion, that not even the Elder Gods were able to prevent the warriors sensational blood lust. It effected other undiscovered realms and worlds which lead to this war with the two realms that were affected most and was at it's peak of supremacy. This is only the end of the beginning, as Shang Tsung puts it. He has worse ploys that he will unleash in the next "season".
Every realm has become one. There are many angry warriors that must do as Shang Tsung pleases or else he will devour the life of their realms. All shall fear the mighty Shang Tsung and participate in his newly created Tournament, as he supposibly said.
War of the Realms
Hint: Pay attention at the very end of the credits you will see a preview of what to come.