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.
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.
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.
The plot could be that Raven is in a dire situation in her world. She discovers an ancient spell that might be able to bring a powerful ally to her side. She decides to use it to summon Naruto. Once Naruto arrives, they face a powerful enemy that is threatening Raven's world. They combine their powers, Naruto's Rasengan and Raven's dark magic, to defeat the enemy.
Well, one possible plot could be that the servant Naruto summons is from a future time. This servant has knowledge of events that are yet to happen in the Naruto world. Naruto then has to use this knowledge wisely while also keeping the servant's origin a secret from others who might misuse it.
Maybe Harry summons Manda because he believes Manda has knowledge about a hidden magical artifact. Manda then guides Harry through a series of challenges to find this artifact which could be the key to saving the wizarding world from a new dark threat.
A possible plot could be that there is a disturbance in the balance of the Naruto world. The sages believe that only a being from another realm can help. Naruto is chosen to perform the summoning. He summons Mordred, and at first, they don't get along because of their different backgrounds. But as they learn more about each other and the true nature of the threat, they form an alliance. Mordred teaches Naruto some new combat techniques, and Naruto shows Mordred the value of friendship and loyalty in his world. Eventually, they defeat the enemy and Mordred may or may not decide to stay in the Naruto world depending on how their relationship has developed.
Well, in such a fanfiction, Naruto might learn unique skills from the summons. For example, he could learn stealth from a cat - like summon or brute strength tactics from a bear - like one.
The fanfiction might start with Ilya performing a summoning spell that she thought would bring something else, but instead, Naruto appears. Since Naruto is always eager to make friends and help others, he quickly bonds with Ilya. They could then embark on a journey to find a way to send Naruto back home. During this time, Naruto could teach Ilya about the importance of perseverance and believing in oneself, just like he learned in his own adventures in the Naruto world.
The plot could be centered around a mysterious quest. Arthuria summons Archer Emiya to help her find a powerful relic that has been lost for centuries. Along the way, they face various foes who also seek the relic. Emiya's ranged combat skills and Arthuria's leadership and swordsmanship complement each other, allowing them to progress through the challenges.
The plot could be centered around a mysterious magical anomaly that Artoria can't handle alone. So she summons Archer Emiya. They then embark on a journey to figure out the source of the anomaly. During this journey, they face many challenges that test their skills and their relationship. Eventually, they succeed in solving the mystery and in the process, become closer as comrades.