Perhaps some ancient evil forces from Gilgamesh's own world that somehow manage to cross over into the Highschool DxD universe could be the main antagonists. These forces might be seeking to destroy both worlds or gain control over them. They could be stronger than the normal devils, angels, and fallen angels in the Highschool DxD world, which would make them a great threat not only to Gilgamesh but also to all the other characters in the fanfiction.
The devils who oppose Gilgamesh's presence in the Highschool DxD world could be main antagonists. They might see him as a threat to their power and influence in the school.
The devils who oppose Grayfia's family could be the main antagonists. They might see Grayfia's brother - in - law as a weak link or a potential threat to their power. So they would try to get rid of him or manipulate him for their own gains.
In certain fanfictions, fallen angels may act as antagonists. They could be trying to disrupt the relationship between Akeno and Issei or simply cause chaos in the devil world where they live.
There could be a demonic entity in the new world. It might be awakened by Gilgamesh's arrival. This entity is used to having its way in the world and sees Gilgamesh as a new obstacle. It could possess other beings to attack Gilgamesh and use the chaos of the new world to its advantage.
Danzo could be a great antagonist in this 'naruto highschool au fanfiction'. He could be the strict school principal who enforces very strict rules and has a hidden agenda. He might not like Naruto's free - spirited nature and try to expel him. Also, Kabuto could be a student who is under Danzo's influence and causes trouble for Naruto and his friends.
In this kind of fanfiction, the Fallen Angels could be main antagonists. They might see Naruto and Sasuke as threats to their plans in the DxD world.
It could be an old enemy of the group who has a personal vendetta against Issei. This antagonist might be jealous of Issei's power or popularity within the group and plots to turn everyone against him. They could spread false rumors or create false evidence to make it seem like Issei has betrayed the group.
The devils who oppose Naruto's presence and his new - found influence in the DxD world could be main antagonists. They might see him as a threat to their power structure and the way things are done in their society.
The Khaos Brigade could be a major antagonist. Their goal of causing chaos would put them at odds with Gohan's sense of justice.
In Gilgamesh Highschool DxD fanfiction, there might be concepts like Gilgamesh forming alliances or rivalries with the devils, angels, and fallen angels in the Highschool DxD world. His vast treasures from his own story could also play a role, perhaps being used as bargaining chips or powerful weapons in the battles that often occur in the Highschool DxD setting.
Maybe a rogue ninja from Gaara's world who somehow follows him into the DxD highschool. This ninja could have a vendetta against Gaara and use the chaos of the DxD world to try and take him down. They could also team up with some of the devils who dislike Gaara's presence to create more trouble for him.