Maybe a story where the powers of Prototype are combined with the Sacred Gears in Highschool DxD. The main character could be a new transfer student who has a Sacred Gear that is somehow related to the Prototype virus, leading to all sorts of chaos and power struggles among the different factions.
One idea could be a character from Prototype having to adapt to the supernatural world of Highschool DxD. For example, Alex Mercer could end up at Kuoh Academy and have to deal with the devils and angels while also trying to figure out his own powers in this new context.
A plot could involve a Prototype - inspired anti - hero who teams up with the main characters of Highschool DxD to fight a common enemy. This enemy could be a new type of threat that neither the devils, angels, nor the Prototype - like being has faced before, forcing them to work together and learn from each other's strengths.
One idea could be to create an alternate universe where the main character has a different set of powers. For example, instead of the traditional Sacred Gear, they could have a power related to time manipulation. This would change the dynamics of battles and interactions with other characters.
One idea could be that Ichigo is somehow transported to the High School DxD world and has to deal with the Devils and Angels there. He might use his Soul Reaper powers in unique ways to solve the problems in this new world.
Perhaps there could be a crossover of the two schools. The students from Beacon Academy and Kuoh Academy could have an exchange program. Yang might get into some friendly (or not so friendly) competitions with the devils in terms of strength, while Weiss could be fascinated by the more formal and complex social structure in the Highschool DxD world.
Maybe in the fanfiction, there's a magical event that links the world of Illya with the Highschool DxD universe. Illya's innocent nature could be a contrast to the more risqué and wild nature of some of the Highschool DxD characters. Her friendship with Issei could start off rocky but then develop into a strong bond as they train together to improve their respective powers.
One idea could be an OC who is a transfer student with a unique power that no one in the Highschool DxD universe has seen before. This power could attract the attention of the main characters and lead to various adventures and alliances.
Perhaps the OC is a skilled musician and Sona, who has an appreciation for the arts, meets the OC at a school concert. They start collaborating on music projects and their relationship blossoms from there. The OC could also have some sort of hidden past related to the supernatural world that Sona helps them uncover.
One idea could be that Naruto, through some sort of interdimensional rift, ends up in the world of Highschool DxD. Ravel could be intrigued by this strange new being with his unique powers. Maybe Naruto has to team up with Ravel to face a common enemy in the DxD world, like a rogue group of devils. His ninja skills would be a novelty there and could help them in battles.
One idea could be that Naruto somehow gets transported to the High School DxD world and has to use his ninja skills in the battles there. Maybe he teams up with Issei and they combine their powers in a unique way.
One plot idea could be Naruto being transferred to the Highschool DxD world and having to adjust to the new school environment while also dealing with the supernatural elements. He could form an unexpected friendship with Ophis, perhaps over their shared experiences of being different from the norm in their respective worlds.
One idea could be that Harry Potter somehow gets transported to the world of Highschool DxD. He could use his magic skills in the unique battles and challenges there. For example, he might use spells like Expelliarmus to disarm the devils or fallen angels during a fight.