Another idea is that Kiritsugu summons Shirou because he foresees a future threat that only Shirou can prevent. This could involve time - traveling elements. Shirou might have to go back in time to change certain events. During this process, he and Kiritsugu would have to work together to figure out how to manipulate time without causing major disruptions.
The plot could start with Shirou being in a desperate situation in his own world. He discovers an ancient spell or artifact that has the power to summon a powerful ally from another dimension, which turns out to be Naruto. Naruto then helps Shirou fight against the enemies that are threatening his world. Along the way, they face challenges that require both of their skills, like Naruto using his Rasengan against magical beasts and Shirou projecting shields to protect them from enemy attacks.
Well, in such a fanfic, Kiritsugu might summon Shirou for a crucial mission. Maybe there's a powerful enemy that only Shirou can defeat with his unique abilities. It could also be that Kiritsugu summons Shirou to pass on some important knowledge or skills. Or perhaps it's a situation where Shirou is the key to saving a particular world or timeline that Kiritsugu is involved in.
One possible plot could be that Irisviel summons Archer Shirou in a world where Arturia already exists. Maybe Irisviel has a specific plan to use Archer's abilities to help Arturia in some great battle or quest. Archer might initially be reluctant to work with Arturia due to their past differences, but as the story progresses, they start to understand each other better and form a strong alliance.
One interesting fanfiction could be where Saber summons Shirou in a modern setting with a twist. For example, instead of the usual Holy Grail War context, it's in a world where magic is more commonplace. Saber might summon Shirou to help her with a different kind of quest, like saving a magical artifact from being misused. The story could explore their relationship development outside of the typical war scenario.
Another theme is the idea of destiny. Often in these fanfictions, their being summoned together is seen as part of a greater destiny. For example, in some stories, they are meant to save a certain world or defeat a powerful enemy. It gives a sense of purpose to their relationship. Also, the theme of self - discovery is quite prevalent. As they face challenges together, they learn more about themselves and their own powers. This is especially true for Shirou as he often discovers new aspects of his abilities when paired with Arturia.
Archer and Arturia would likely start off with a bit of friction. Archer, being from a different time and having his own set of beliefs, might clash with Arturia's more traditional knightly values. However, as they face challenges together, they would gradually learn to respect each other. Irisviel would be the mediator, guiding their interactions and making sure they stay focused on the task at hand.
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.
At first, their relationship might be one of master - servant formality. Shirou would be cautious and respectful, while Merlin would be somewhat aloof. But as time goes on, Shirou's determination and pure heart could win Merlin over. Merlin might start to see Shirou as more than just a master, but as a friend or someone worthy of his real help.
A plot could be centered around Shirou summoning Morgan to help him in a magical tournament. Morgan, being a powerful figure, has her own motives for participating. Along the way, Shirou discovers that Morgan has a connection to his past that he was unaware of. As they compete in the tournament, they face opponents who force them to work together and rely on each other's strengths, leading to a deeper understanding between them.
Their relationship could develop in an interesting way. Since Shirou is often self - sacrificing and Morgan is a powerful and complex character. When Shirou summons her, she may see him as a tool at first. However, as she witnesses his unwavering beliefs and courage in the face of danger, she might start to soften towards him. Maybe she begins to protect him in battles, and they start to share their thoughts and feelings, slowly building a deeper connection.