They could possibly retcon Raiden even visiting Quan-Chi in MK9
Doubt that as well, since Quan Chi obviously has some kind of thing going on with Kitana. Notice how we only ever hear 2 lines in their introduction, where as the standard is a 3 line back-and-forth. We are missing something in that first quote that Kitana says, probably has to do with plot details.
Also, Scorpion knows about Quan Chi's deception about his clan through his dialogue, so that means MK9 stuff had to have happened like Raiden talking to Scorp and the story endings.
This leads me to believe that something happened, perhaps the merging of the realms and the ending of Shao Khan's reign voided his contract with Quan Chi. However, certain people of importance (Specifically importance to Liu Kang) were kept tied directly to Quan Chi through an act of Shinnok. Scorpion was freed of his master, probably a gift of the elder gods. A gift Quan Chi was not pleased to have happen. After manipulating Forest Fox (with Shinnok's help) he spurs Scorpion back into battle, but not before bringing about Takeda's introduction into the bloodsport.
As the future unfolds, Raiden bears witness to the return of old foes and the fall of old friends as well. One such friend is Fujin, who falls in battle at the Elder God's Palace by a hooded individual. He reaches out to his old allies, realizing that Shao Khan's contract was relinquished by the new Khan, Kotal. Some respond, namely the progeny of Johnny Cage and Sonya Blade, as well as the daughter of Jax. Others, however, cannot be reached. Liu Kang, Earthrealm's greatest ally, is missing after his murder at the hands of Raiden, and Kung Lao has also barred contact, disappearing from the Thunder God's eyes.
In this new, ruthless time, Earthrealm stands once again on the brink of disaster. Will Raiden be able to bring about peace again? Or will Earthrealm give birth to its own demise?
Will the fallen Elder God Shinnok reclaim his place, or will Raiden be able to hold off his brutal advance?
Will Kotal Khan break the delicate balance, and bring new life to his Khan title? Will an old ruler, with more to gain from this turmoil, return to claim his rightful throne?
Will the Black Dragon finally show their hand, pick a side, or come out on top after the work has been done for them?
Only time will tell.
At least thats what I gather from it. I'm probably WAYYYYYYYYYYYY off.