How did the humans come back to life?


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Shao Kahn took all of the souls of every single person on Earth except Raiden's chosen and it seems implied they were completely assimilated too. How did they ever come back after the invasion..? Perhaps the Elder Gods restored them?
They didn't come back to life. According to the Mortal Kombat 3 wiki: "When Sindel is reincarnated in Earthrealm, Shao Kahn reaches across the dimensions to reclaim her, and as a result, Earthrealm gradually becomes a part of Outworld, instantly stripping billions of their souls. Only a few are spared, as Raiden protects their souls." So Raiden was able to protect a few of them.


Edit: I just saw that you meant after the invasion. I believe it's implied that once Shao Kahn is defeated (see Shang Tsung's ending for example) that the souls are released by Kahn back into the world.
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