It could be Orochimaru. He is always seeking power and the strange and powerful abilities of the Ghost Rider might be something he desires. He could try to capture or study the Ghost Rider to gain an edge in his own plans for power and immortality.
It could be a powerful dragon hunter. This person would see Naruto's dragon as a prize to be captured or killed. They might have a personal vendetta against dragon riders in general.
A powerful dark wizard from the human world who has found a way to cross over into Equestria. He wants to harness the magic of the Elements of Harmony to increase his own power. He sees the Ghost Rider as a threat to his plans and tries to eliminate him while also causing chaos in Equestria.
It could be a powerful devil who sees the Ghost Rider as a threat to his plans in the school. Maybe this devil wants to take over the school or gain more power among the students, and the Ghost Rider's presence and his sense of justice stand in the way.
It could be an evil spirit that wants to use Naruto's new ghostly form for its own dark purposes. Maybe it tries to control Naruto and make him do evil things.
Another option could be a new character created specifically for this fanfiction. This character could have the ability to manipulate both the ninja and the Ghost Rider elements, and wants to use that power to rule over both worlds. So, they would be the main adversary that Naruto and others have to face.
A powerful dark wizard could be the main antagonist. He might be jealous of the dragon rider's powers and the bond with the dragon, and wants to break that bond and steal the rider's powers for himself.
Perhaps a powerful sorcerer who wants to capture the black horse for his own dark purposes.
Dormammu could also be a formidable antagonist. His dark magic and his desire to expand his dark dimension could put him in conflict with Ghost Rider. If there's a crossover with the Fantastic Four world, he could use his powers to try and take over Earth while Ghost Rider tries to stop him, and the Fantastic Four might get caught in the middle.
A good antagonist could be a character from the 'Resident Evil' universe, like Albert Wesker. His superhuman abilities and evil plans for global domination would pose a huge threat to Alex Rider. Alex would have to use his wits and skills to stop Wesker's bio - terrorist plans.
It could be a powerful and shadowy figure from Wolf's past, like an old military commander who has gone rogue. This person might have a vendetta against Wolf for some past betrayal and sees Alex as a way to get to Wolf, using Alex's importance in the spy world as leverage.