Before I state my take on the story, I want to explain why I'm doing it:

-Because I'm more of a retro gamer and mostly like classic games better than new games.
-Because this way I don't end up hating Mortal Kombat 2011 and fearing the direction the series is going.

There are three versions of the Mortal Kombat storyline:
1. The canonical story of Mortal Kombat 1, 2, 3 + Ultimate + Trilogy, and 4 + Gold. The story progresses as it originally did, and when Liu Kang defeats Shinnok at the end of MK4, Earthrealm is saved forever, and everyone lives happily ever after. The End.

2. The "What-If?" story of Deadly Alliance, Deception, and Armageddon. In my view of the canonical story, Quan Chi is captured and killed by Scorpion at the end of MK4, thus Scorpion truly avenges his family and clan. But since I consider MKDA a "What-If?" story, Quan Chi is allowed to form the Deadly Alliance with Shang Tsung in this new timeline, thus starting the chain of events that lead to Armageddon and Earthrealm's impending doom. Which leads to...

3. The "Alternate Take" of the "What-If?" story, a.k.a. Mortal Kombat 2011. In my view, the Alternate Take can't really be the canonical story all over again, partly because things were already messed up BEFORE Raiden messed things up. For example: Nightwolf, Kitana and Jade, Sektor and Cyrax, Jax, Quan Chi, and Baraka were never part of the original tournament. So I base it on the "What If?" story, because that's where it fits better.

That's my take on the storyline. You're welcome to disagree with me, but just remember: I've loved Mortal Kombat ever since I was a child, and by doing this take, I'm trying to defend that love and keep it going, whether the series goes for better or for worse.