One way could be through a powerful magic - ninjutsu hybrid spell. Maybe a character with knowledge of both worlds accidentally creates a portal that merges the two. For example, if a shinobi in Naruto world somehow gets hold of a magic item from Highschool DxD and activates it in a wrong way.
Another approach could be a shared enemy. Suppose there is an entity that exists in both universes in a different form. Writers could create a story where the characters from Highschool DxD and Prototype have to team up to defeat this entity. This would require them to understand each other's powers and work together, leading to a lot of character development and exciting action scenes.
It's hard to say for sure, but Naruto himself could be a strong contender. His vast array of jutsu and his ability to grow in power constantly could make him extremely powerful. He has faced incredibly tough opponents and come out on top in the Naruto universe, so in a merged universe, he could use his skills to take on the devils and other beings.
It could be Issei if he were to gain Naruto's abilities. He already has his own set of powerful skills in the DxD world. Adding Naruto's chakra and jutsus like the Rasengan or the ability to summon toads would make him extremely formidable.
I'm not sure if there is specific fanfiction directly involving both Naruto and Grayfia from Highschool DxD. Fanfiction can cover a vast range of combinations and crossovers, but this particular one might be quite rare. You could try searching on specialized fanfiction websites to see if any exist.
Probably Great Red from Highschool DxD. He's already an extremely powerful being in his own universe. If he were to encounter the power of the Omnitrix and all the alien forms in Ben 10, he could potentially assimilate or use those powers in some way to become even more powerful.
It's hard to say for sure, but some might argue that it could be Julius Novachrono from Black Clover. His time - magic is extremely powerful, and he could potentially manipulate time to his advantage in battles against the Highschool DxD characters. He could stop time and land fatal blows before his opponents even realize what's happening.
A possible way for their worlds to merge in fanfiction is through a reincarnation plot. What if some of the Naruto characters were reincarnated in the Highschool DxD world? Naruto himself could be reborn as a devil or an angel. This would completely change the power balance and relationships in the Highschool DxD world. Rias would have to deal with this new Naruto, who still has his ninja spirit but now has to adapt to the rules and powers of the new world.
One common theme is her loyalty. Grayfia is known for her loyalty in the series, and fanfictions often explore this aspect further, like how she balances her loyalty to different characters or factions. Another theme is her power. Writers like to show her using her magic and skills in different situations.
One common theme is loyalty. Grayfia is often portrayed as being extremely loyal in these fanfictions, whether it's to her superiors or to her new friends in the high school setting. Another theme is mystery, as her character often has secrets that are slowly uncovered throughout the story.
Well, one way is through character exchanges. Imagine a character from Naruto like Naruto himself ending up in the Highschool DxD universe and meeting Leviathan. He could introduce his ninja skills to that world and also learn about the devil powers. Another way is to have a common enemy. For instance, a new threat that can only be defeated by combining the unique powers from all three, like the Rasengan combined with a Highschool DxD power against an enemy threatening Leviathan.