I think an interesting point that should be here, and I am surprised it hasn't been brought up yet, is the characters locked up in the prison. According to the storyline, Reptile is the body that Onaga used to come back in, yet here he is locked up in the prison. Shao Khan is supposly died, yet, here he is in the prison locked up. It seems that Midway cannot even keep up with their storylines anymore.

The people locked in the prison have nothing to do with the MK story.
The people in the prison are just random people who have been important in MK history, no matter what they are doing now.

That makes the game even more inconsitent then IMO. I am not bagging the game for being bad, its just that the prison thing should off been more consitent with the story I think.

As I just posted in another thread, Kahn is dead. It says so right in Reptile's Konquest part of Deadly Alliance. He FINDS Kahn DEAD. That's when he begins to wander Outworld during which he finds Nitara.

True, but Liu Kang was also dead and now he is Deception. So I am sure if Liu Kang can be back in MK then Shao Kahn can also. Also all the people in Edenia said Sindel is in hiding until Shao Kahn is removed from power.

If I'm not mistaken, it's rather common for MK characters to come back from the dead.

Here's what I think: It's either Kahn, or Reiko pretending to be Kahn. Kahn's a tyrannical emperor; it's bound that he'd have a whole lot of people after his ass. Since Konquest mode's established that Reiko has a fetish for wearing Kahn's helmet (and, hence, explaining his ending in the home version of MK4), Kahn could've used this info to make Reiko his decoy, for whenever he feels a sneak attack on his person coming on. With some magic, it would be easy to make Reiko look like Kahn, and have his true identity be undetectable by any sorcerers like Shang Tsung. If Shang and Quan Chi didn't check the body to make sure it was really Kahn, then Reiko's deception would be secured. Same with Reptile: we already know he's easilly distracted and not prone to noticing detail, so it would be easy to fool him into thinking that the Reiko-decoy was actually Kahn.

well in haviks ending he uses dragon kings heart to reanamate the dead so who does he bring back shao kahn. This prolly definetly gives away the boss for mk7 so its prolly kahn because no other boss was hinted in the other endings. then also in mk7 prolly havik will be the sub boxx but only more tougher.