The power systems could also be integrated through genetic manipulation. Since Prototype has a lot to do with biological mutations, a scientist or a character with knowledge of both worlds could try to engineer a way to give Highschool DxD characters Prototype - like powers on a genetic level. This could lead to some really interesting power combinations and new abilities that are unique to the fanfiction.
Another approach is to consider the energy sources. In Prototype, there's the virus as a source of power. In Highschool DxD, there's magic and spiritual energy. Maybe the virus could be a corrupted form of magic in the fanfiction. Characters could then try to either purify or control this 'viral magic' and use it in combination with their existing powers from the Highschool DxD universe.