One idea could be that Naruto is summoned into the Fate universe during the Holy Grail War. He might be mistaken for a Servant at first. His unique ninja abilities would disrupt the normal flow of the war. For example, his Shadow Clone Jutsu could be used to confuse the enemy Masters and Servants.
One interesting plot idea could be that the Servants from Fate Stay Night end up in the Naruto world. For example, Saber could team up with Naruto. Saber's noble and just nature would blend well with Naruto's determination to protect his village. They could face off against common enemies like Orochimaru, who might be interested in the power of the Servants. Another idea is that the concept of chakra in the Naruto world could interact with the magic in Fate Stay Night. Maybe a mage from the Fate universe tries to study chakra and finds a way to combine it with their own magic system, creating a whole new type of power. A third plot could involve the Holy Grail War taking place in the Hidden Leaf Village. The ninjas would be both intrigued and cautious about this strange new event, and the Servants would have to navigate the politics and unique environment of the village while fighting for the Grail.
One idea could be a crossover with the Justice League. Dr Fate could use his magic to help the League against a powerful magical threat that they can't handle alone. Maybe a dark sorcerer from another dimension is trying to invade Earth, and Dr Fate's knowledge of ancient magic is crucial in devising a counter - attack.
One idea could be that the Servants from Fate are transported to the Halo universe. For example, Saber could find herself in a battle against the Covenant. Her noble phantasm could be a powerful weapon against the alien foes. Another plot could involve Master - Spartan team - pairings. A Spartan could be paired with a mage to fight a common enemy that threatens both the Halo and Fate worlds.
A cool concept for a 'naruto fate crossover fanfic' could be the appearance of the Akatsuki in the Fate world. They might be after the Holy Grail for their own purposes, like using it to gain ultimate power or to bring about a new world order. Pain could use his Rinnegan abilities in ways that would surprise the Fate characters. Also, the concept of ninjas from Naruto world learning about the different classes of Servants in Fate, like Saber, Archer etc., and how they would strategize against them.
For 'fate crossover fanfiction', you could consider a crossover with 'One Piece'. The Servants might be pirates or marines, sailing the Grand Line. A 'Fate' and 'Fullmetal Alchemist' crossover would also be cool. Picture Servants trying to solve the mysteries of alchemy. There's also potential in a 'Fate' and 'My Hero Academia' crossover, with Servants having Quirks.
Maybe a time - travel based crossover. A character from Fate Kaleid Liner accidentally travels back in time and meets the younger versions of other characters in the series. This could lead to changes in the timeline and they would have to work together to fix any potential disasters that their meeting has caused, all while trying to find a way back to their own time.
Maybe Arthur Pendragon gets transported to the Fate world and his presence disrupts the normal balance of power. The mages in the Fate universe might see him as a threat or an opportunity. He could end up being a wild card in the Grail War, not bound by the normal rules of Servant summoning. His noble phantasm, Excalibur, could be a game - changer in battles against other powerful Servants.
A possible plot for this crossover fanfiction could be centered around the concept of the 'ideal'. In Fate Stay, each Servant has an ideal they fight for, and in RWBY, the characters also have their own beliefs and goals. So, a story could be crafted where the characters from both universes have to compare and contrast their ideals. Maybe some of the Fate Stay characters are confused by the concept of the Grimm and the Huntsmen/Huntresses' role in RWBY, while the RWBY characters are intrigued by the Servant - Master relationship in Fate Stay.
A possible plot could be that Jack the Ripper's true identity in the fanfiction is actually a corrupted form of an otherwise noble Servant. Maybe he was a heroic figure in the past but was corrupted by a powerful dark magic. A group of Fate characters could then be on a quest to find a way to reverse this corruption. They would have to face not only Jack the Ripper's deadly attacks but also the political and social unrest in the London setting of the story. The fanfiction could also explore the psychological aspect of how the Ripper's mind works and how the Fate characters react to his extreme violence.
Maybe a character from Blue Exorcist gets summoned into the Fate universe by mistake. They then have to adapt to the new rules and magic there, and form alliances with the Fate characters to find a way back home. Along the way, they discover new aspects of their own powers.