First, decide on the main characters and their initial situations. Then, plot out key events in chronological order. For example, if it's a story about a hero's journey, start with his ordinary life, then the call to adventure, and so on.
Another concept is a love story involving an MK11 guest character. They could fall in love with a character from the Mortal Kombat world. This love could be a forbidden one, as their two worlds have different values and rules. Their relationship would face many challenges, both from the outside world and from within themselves as they struggle with their feelings and loyalties.
Scorpion and Sub - Zero are main characters. Scorpion is known for his hellish powers and thirst for revenge at times. Sub - Zero has his ice - based abilities. Liu Kang also plays a significant role, being a powerful fighter in the Mortal Kombat universe.
Create an engaging plot. Don't just rely on the fighting aspect of Mortal Kombat. Maybe there's a mystery that the guest character needs to solve, like a conspiracy within the MK11 tournament. You can also add some twists and turns to keep the readers interested.
Obviously, MK and Mandrake are the main characters. MK is the one who gets kidnapped, so he is likely to be the protagonist in the sense that the story will probably focus on his struggle and how he deals with the situation. Mandrake, on the other hand, is the kidnapper, so he is the antagonist. He is the one creating the conflict in the story.
Well, the canon status of MK comics isn't straightforward. It might be canon within certain story arcs or universes, but not across the board. Different interpretations and continuities can come into play.