This is really wierd and has had me thinking all day so far. I heard a storyline mentioned that Onaga discovered the bodies of slain warriors, revived them and imprisoned them - this is how Kung Lao, Sonya, Cage etc are supposed to be alive after Deception (so they can be in MK7)
I noticed today that Shao Kahn was also down there in a cell! I was wondering whether this could be a brother or clone, since I was controlling Havik at the time and he doesn't resurrect Kahn until after the game is done! In any case, Onaga needed to die for Havik to revive Kahn, so in this case Onaga couldn't very well have imprisoned him...
I suppose it's possible that Havik's ending might not be considered canon by the time MK7 comes out after all - since Kabal's conflicts in any case - but this still does not rule out Shao Kahn's grand return in MK7...
Onaga may very well have resurrected him! Don't forget, these two go way back and Kahn was once Onaga's advisor. Kahn was the one who killed Onaga (he poisoned him), which makes Onaga unlikely to trust Kahn, and very likely to harbour a grudge against him. Perhaps Onaga had intentions to greatly punish Kahn once he became overlord of the One Realm...
Anyhow, what we now have are TWO plausable reasons why Shao Kahn should definatly be alive (if not the boss) in Mortal kombat 7!
Unless Onaga just cloned him!
Peace!