Honestly, I feel confident in believing Shinnok is going to be the big bad. Theories have been discussed on MKO, and it's all starting to make sense to me now.
-When MK1 Raiden captures Shinnok in the amulet, that is a flashback of something that happened shortly after MK9. The threat has been taken care of.
-Jump a little bit ahead, and Mileena is deposed from the throne of Shao Kahn somehow.
-Kotal Kahn assumes the throne, gathering guards that were once with Shao Kahn, as well as Erron Black.
-The amulet is apparently lost from Raiden, wherein Mileena takes possession of it.
-Gathering the Tarkatan, Rain, and another couple players (Reiko?), she mounts an offensive against Kotal Kahn.
-The trailer shows her beginning to use the amulet in a similar fashion to how Raiden used it on Shinnok, where she hopes to imprison Kotal.
-She's unaware of Shinnok's presence in the amulet, and the absorption of Kotal fails, and unknowingly releases Shinnok on both Kotal and Mileena.
-Raiden is aware of all of this possibly taking place, hence his grave warning of the amulet.
-Raiden tells Cassie to lead the rest of the Special Forces group in hopes of finding Mileena, and or possibly reclaiming the amulet before she can use it. This is why they meet with Kotal, and Kotal with Kano in hopes of finding Mileena.
-Shinnok is loose, and there you have it.
That of course is 100% conjecture.