The ending with Blaze after Armageddon could be used to set up the collision of world with MK and DC.
Something like instead of stripping the powers of all kombatants or killing all kombatant, the defeat of Blaze had a different result. While Blaze stripped the powers of the kombatants, the combined powers were so strong that an almighty demon sorcerer from a different universe sensed it. Knowing that possessing this almighty power would make him the ultimate ruler of his universe, Ra's Al Ghul made an effort to disrupt the process of Blaze and divert those combined powers to himself.
He used the powers of the Lazarus pits or tapped in the powers of kombatants in his universe to open a portal to this universe. But Ra's Al Ghul couldn't properly take over the process or properly handle the stream of combined powers so the diversion of the powers went wrong.
Some kombatants of the MK were killed because more than just their powers were taken. Other MK Kombatants were given their powers back while some of the powers went to kombatants of the other realm (Batman etc).
To set the right balance back, these kombatants must battle each other to save both universes.
Or a more simple and traditional MK approach can be taken. Shao Kahn grew annoyed of failing to take over the earthrealm. By communicating and planning with a sorcerer of a different universe (Ra's Al Ghul) Shao Kahn set up a different plan. Instead of again trying to take over earthrealm of his universe he opened a portal to a different universe through combined efforts of Tsung and Ra's Al Ghul. Shao Kahn now will try to take over earth of a different Universe by means of Mortal Kombat, because this Universe is not actively protected by one Elder God. Some kombatants of DC earth are chosen to participate in the following MK. Some kombatants of MK universe are joining this MK to stop Shao Kahn or for different reasons
(eg Sub Zero joins to defeat Mr Freeze and enhance his freezing power,
Shang Tsung to gain Ra's Al Ghul secret to immortality,
Ra's Al Ghul joins because he was promised by Shao Kahn to be ruler of DC earth after the MK but got a vision that Shao Kahn would betray him and merge DC Earth with Outworld and suck its powers,
Reptile searches for Killer Crock because Killer Crock's reptilian evolution holds the key to Reptiles species next evolution to a stronger more dominant species. Or because reptiles species wants Killer Crock as their leader and Reptile will prove that instead he is worthy of leadership).