In a nutshell, I see it as an alternate timeline with details retconned in and out.

Whilst it is an alternate timeline there is a chance that the elder gods acknowledge all the time alterations of Raiden giving us the feeling that it is still the same old timeline. It would be cool to find out that time doesn't run in the Void and Heavens for instance and some fighters of the old timeline would jump into the new timeline from there. However, the most of the fighters were fighting around the pyramid, but just my two cents.

I don't think the writers that thought of the story in this game even went that deep to examine if this will be the "same MK universe" or "a parallel universe" or whatever. They just said "Hell everyone died in MKA so let's make Raiden send a message to the past and see what happens!".....

They've described the game as a reboot. And the amount of stuff they changed backs that up. It's like the difference between Pine Star Trek and Shatner Star Trek, or Pre-Crisis and Post-Crisis in the DC Universe, where in this case, the "Crisis" is Armageddon.

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This is by far, the darkest intro of Mortal Kombat ever! (More dark than DA) That's what makes it cool

Dark cool intro sums it up.

Who's that at the end of the pyramid just after Liu Kang, Shang Tsung?

Old Man Tsung, yeah.

@Jaded-Raven Do you prefer good Jade or bad Jade?
I still wish Jade and Kitana would remain bad guys, its so cliche when the bad girls turn good, reminds me of like almost every James Bond movie, but there are some ones where the bad girls stays bad.

Jade is nor good or bad. She's Jade. And so far I like all she's done.