In fanfiction, Shirou could be exposed to a different moral code during the 4th Grail War. Maybe he meets a group of mages who have a more flexible view on right and wrong. This exposure could make him question his own beliefs and lead to a significant change in his character as he tries to find his place in this new moral landscape.
He would likely become more cynical. In the normal story, Shirou is fairly idealistic. But as an Avenger, he'd see the darker side of things more often. For instance, he might not trust people as easily as he used to. He would always be on the lookout for hidden motives.
Another plot could involve Shirou getting a glimpse into the past of the Grail War through some sort of magical artifact. He discovers secrets that were long buried and this knowledge could either help him in the war or put him in greater danger as others may want to silence him.
First, you can give Shirou a new backstory. Maybe he has a different family history or a unique experience that shaped him. This will make his character more distinct. For instance, if he was raised in a different part of the world, his views on heroism might be different.
In this fanfic, Emiya might be more assertive. In the original, he is often reserved and follows his own code quietly. But here, perhaps the circumstances of the 4th Grail War force him to be more outspoken and take more initiative. He could be more open about his feelings and motives, which is different from his rather mysterious nature in the original. For example, he might directly tell other Servants his thoughts on the Grail War instead of keeping them to himself.
Some fanfictions might focus on Shirou's struggle with his ideals in a more extreme way. For example, he could face a situation where his ideal of being a hero for everyone conflicts with the reality of the Grail War, and he has to make difficult choices that really test his beliefs.
Another plot idea might be to focus on Shirou's internal struggle during the Grail War in more depth. Show how his ideals are tested not just in battle, but also in his interactions with other Masters and Servants. Maybe he has to make some really tough moral choices that could change the course of the war.
His projection magic might be affected by the different magical rules in the Highschool DxD world. Maybe it becomes more powerful or has some new limitations. For example, projecting holy swords could have a different energy cost or be more effective against certain types of devils or fallen angels.
Naruto would likely become more diplomatic. As an emperor, he can't just rely on brute force like he sometimes did as a ninja. He'd have to think about the long - term consequences of his actions for the whole empire. So, he'd develop better negotiation skills.
His relationship with Saber could change significantly. She might see him in a new light, as an equal or even a superior in terms of combat and strategic thinking if he applies his gamer skills. He could be more confident around her and their interactions could become more of a partnership where they exchange ideas on battle tactics.
The Emiya ending in the Fourth Grail War fanfiction often shows his complex character. He is a hero with a strong sense of justice. In this ending, he might face difficult choices. Maybe he sacrifices himself to save others, which is in line with his selfless nature.