One idea could be that Naruto characters are somehow transported to the FMA world and have to adapt to the rules of alchemy. For example, Naruto might be intrigued by the concept of equivalent exchange and try to apply his ninja way to it. He could learn alchemy and use his chakra in unique ways to manipulate it.
Perhaps Sasuke could be paired with Edward in an adventure. Sasuke, with his Sharingan, might be able to see the flow of alchemy in a different way than others. Edward, on the other hand, could teach Sasuke about the scientific principles behind alchemy. Together, they could face a common enemy that is threatening both the Naruto and FMA worlds.
One idea could be that Greed finds himself in an alternate universe where the rules of alchemy are slightly different. He could then try to adapt and use this new knowledge to his advantage, all while facing new and unexpected enemies. Another plot could involve Greed teaming up with characters from another fandom in a quest for a powerful and mysterious object that exists in both worlds.
One plot idea could be that Ichigo somehow gets transported to the FMA world. He might initially be confused by the alchemical rules but then use his Soul Reaper powers in unique ways. For example, his Zanpakuto could be seen as a form of alchemical weapon, and he could fight alongside the Elric brothers against the homunculi. Another idea is that the Philosopher's Stone has some connection to the Hollow within Ichigo, and characters from both universes have to work together to prevent a catastrophic event.
Well, a cool plot could be that the Death Eaters are interested in the power of alchemy. They try to capture Edward to force him to use alchemy for their evil purposes. Harry, Ron, and Hermione then rescue him. In return, Edward offers to help them with his alchemical skills in their fight against Voldemort. For example, he could use alchemy to create unique magical items or barriers. Also, Alphonse could befriend some of the Hogwarts ghosts and learn about the secrets of the castle from them, which could be useful in the fight against the dark side.
I think Naruto himself would be really interesting. His positive and determined attitude would contrast with the often darker and more complex world of FMA. He could bring his unique brand of ninja spirit and try to make friends with the characters in FMA. His ability to use chakra and his various jutsu would also create some really cool interactions when faced with the alchemists and their powers.
One idea could be a Naruto and One Piece crossover. Naruto and Luffy could meet and have to team up to defeat a common enemy that threatens both their worlds. Maybe a powerful dark force that can manipulate the sea and the land.
Well, a really cool concept could be a villain that threatens both the Naruto and DBZ universes. So, characters from both sides have to team up to defeat this powerful foe. Imagine Vegeta and Sasuke having to work together, despite their initial differences. Also, there could be a story where the Dragon Balls are somehow transported to the Naruto world, and Naruto and his friends try to figure out what they are and how to use them.
A really interesting fma crossover fanfic idea might be with the world of Fullmetal Alchemist and the Lord of the Rings. Imagine the Elric brothers in Middle - earth, facing the challenges there. They could use their alchemy skills in a world filled with magic, elves, and orcs. It would be a very unique combination as the concepts of alchemy and the magic in Middle - earth are quite different.
In a Naruto Marvel crossover fanfiction, it could be interesting if the X - Men visited the Hidden Leaf Village. Naruto might be fascinated by the mutants' powers and their struggle for acceptance. He could compare it to the discrimination some ninja faced in his own world. The X - Men could also learn from the ninja's stealth and combat techniques. Wolverine, for instance, might spar with Rock Lee and learn some new hand - to - hand combat moves, while Cyclops could study how the ninja use their eyes in combat, like the Sharingan.
One idea could be that Naruto characters end up in the world of Danmachi. For example, Naruto himself could be mistaken for a new type of adventurer with his unique skills like shadow clones. His clones could be used to explore dungeons more efficiently, confusing the locals. Another idea is that Sasuke, with his Sharingan, might be able to quickly analyze the monsters in the Danmachi dungeons, giving him an edge in combat. And Sakura could use her medical ninjutsu to heal the injured adventurers in the world of Danmachi, which would make her a highly sought - after healer.
Maybe the Akatsuki members could be a villainous wrestling gang. They could use their unique abilities, like Sasori's puppet techniques as part of their wrestling moves. Picture Sasori controlling puppets to attack his opponents in the wrestling ring while the referee is trying to figure out if it's legal or not.