I predict the new story will be similar to games like Sonic Generations and the new Transformers: Rise of the Dark Spark games, being basically cross-dimensional and involving different MK characters from different eras...

Three reasons:
1. The supposed confirmation there will be multiple versions of the same character (such as both MK3 Sub-Zero and MK9, possibly)

2. Ed Boon's (as usual) vague tweet about how it will both be a continuation of MK9 as well as an entirely new story, but it's "hard to explain".

3. The absolute CATASTROPHIC MESS of an ending that MK9 had, and seeing as we've got Subby back in the teaser, there's going to be some in-universe ret-conning, especially since most of the character were canonically dead at the end of the last game.

Perhaps maybe Raiden will once again try to JJ Abrams his way out of Armageddon, but it will cause an actual rift that splits reality in two existing dimensions at the same time, making past and future collide.

As a little joke, Boon also said the "X" has multiple meanings, as this could be the MK version of the latest X-Men film :P