Maybe a powerful demon that has been lurking in the shadows of both universes. This demon is attracted by the unique magic in both Coraline's and Norman's worlds. It starts to possess the people and creatures in both places, and Coraline and Norman must find a way to exorcise it. The demon could be very cunning, disguising itself as friendly beings at first.
The main villain could be a corrupted spirit that was once a good protector of both worlds. But something went wrong, and it became twisted. It now wants to erase all the good in both Coraline's and Norman's worlds and replace it with its own dark vision. It has the power to manipulate the minds of the people and the supernatural beings, making it a very difficult enemy to face.
A plot could involve Coraline getting lost in Norman's town and Norman has to help her find her way back home. Along the way, they discover that there are some common elements in the spooky things happening in both their places. For example, the same kind of magic or curse is at work, and they use their unique skills to figure it out. Norman with his ability to see ghosts and Coraline with her courage and inquisitive nature.
The most obvious main antagonist could be the Other Mother. She is already a menacing figure in the original story. In a fanfic where Coraline loses the game, the Other Mother could use her powers to manipulate the game in such a way that Coraline has no chance of winning. She might change the rules mid - game or create illusions to deceive Coraline.
It could be a powerful demon that has the ability to absorb the powers of others. This demon has been observing both Gohan and Naruto from the shadows and wants to take their powers to become invincible.
A new villain could be created specifically for this fanfic. Maybe an interdimensional being that senses the strange energy fluctuations caused by Gohan's training of Naruto. This being, fearing the new power that Naruto might gain, decides to invade Naruto's world to stop the training and take over the world for itself.
It could be Frieza. Frieza is a powerful and evil character from Goku's universe. He might see the combined power of Naruto and Goku as a threat and try to eliminate them. He could also be interested in the unique powers that Naruto has, like the Nine - Tailed Fox's chakra, which he might want to use for his own evil purposes.
A possible main villain could be an evil ninja who has somehow managed to harness dark magic similar to that which the Monkey King once faced. He could be using this magic to try and take over both the ninja world and the world of the Monkey King.
One common theme could be the exploration of unrequited love, just like in many other fanfic. The characters in 'Paranorman' might be put in situations where they have feelings for someone but are afraid to express them due to the nature of their relationship or the circumstances around them.
Obviously, Villain Deku would be the main antagonist. Since he has turned to the dark side, his actions and motives would be in direct opposition to Jirou and the values of the hero world she represents.
It could be Kronos from the Percy Jackson universe. He could somehow find a way to cross over to Daenerys' world and try to take over. He would see her dragons as a great source of power and want to control them for his own evil purposes. Daenerys and Percy would have to put aside their differences and combine their powers to stop Kronos.
The Red Skull could be the main villain. He could team up with some other super - villains or get his hands on some kryptonite - like substance. He would try to use his knowledge of Captain America's past and Superman's weakness to defeat them. He wants to rule the world and sees these two heroes as the biggest obstacles in his way.