Well, one possibility could be that Naruto characters are transported into the Mortal Kombat universe. Naruto, with his Rasengan, could face off against Sub - Zero's ice powers. Maybe they have to fight in Mortal Kombat tournaments to find a way back to their own world. It would be interesting to see how Naruto's ninja skills stack up against Mortal Kombat's brutal fighting styles.
The plot could involve the Mortal Kombat fighters being curious about the strange new arrivals from the Naruto world. They might initially see Naruto and his friends as threats. However, as they learn more about their powers and motives, they could team up. For example, Sasuke's Sharingan could be used to analyze the Mortal Kombat opponents' moves, while Scorpion might teach them some of his hellish combat techniques in return.
In this fanfiction, perhaps there is a greater evil that threatens both universes. The Naruto characters and Mortal Kombat fighters have to put aside their differences. Characters like Sakura could use her medical ninjutsu to heal the Mortal Kombat warriors in between battles. And Raiden from Mortal Kombat could use his godly powers to help Naruto and his friends understand the strange new rules of the Mortal Kombat world.