First, consider the setting. A Naruto - style world could be merged with the pirate - filled seas. The assassin part comes in with the character's motives. He could be an outcast ninja from Naruto's world who finds a new life among pirates but still uses his ninja assassination skills. He might have to fight against other pirate crews or even sea monsters using his Naruto - inspired jutsu and assassin techniques. This combination would create a really unique and exciting fanfiction.
A highly trained assassin with both ninja and pirate skills could also be the most powerful. Imagine an assassin who has mastered the art of silent killing like a ninja but also has the knowledge of poisons and navigation like a pirate. This character could move in the shadows, taking out opponents without being detected, and using their diverse skills to outwit any enemy, be it a powerful ninja like Naruto or a fearsome pirate captain.
In fanfiction, you can also combine their storylines. Say, the plot of 'The Lion King' could be merged with Naruto's journey to become Hokage. Simba's struggle to take his rightful place as king can be paralleled with Naruto's efforts to gain the respect of the Hidden Leaf Village and become its leader. There could be a common enemy that both Naruto and Simba have to face together, something that threatens both the pride lands and the ninja village.
The settings can be combined too. You could create a new world where the Naruto universe and the remnants of Krypton co - exist. Maybe there's a city in this new world where ninjas and Kryptonians live side by side. Naruto could then explore this new place, learn about Kryptonian technology, and use it to enhance his own ninja tools or techniques.
One way is to have the characters from Naruto join a peerage structure similar to that in Bleach. For example, the Hokage could be like the king of the peerage. Then, the jutsu of Naruto characters can be compared or integrated with the powers in Bleach. So, a Rasengan could be equivalent to a certain level of reiatsu - based attack.
One way to combine them could be in a crossover universe. Percy Jackson, with his demigod powers, could meet Naruto, who has his ninja abilities. If Percy was the son of Hera in this fanfiction, perhaps Hera could send Percy on a quest that somehow leads him to Naruto's world. For example, a powerful artifact from the Greek gods has been lost in Naruto's world and Percy has to retrieve it. Along the way, they could learn from each other's skills and cultures.
Another possibility is to have the characters from the Karakuri Circus be transplanted into the Naruto world. They would have to adapt to the ninja society. The Karakuri puppets could be seen as a new type of weapon or tool in the Naruto world. And the circus performers could use their unique skills to either help or cause trouble in the ninja villages.
Another way is to have Naruto fuse his chakra with someone who has the ability to use Susanoo, like Sasuke. They could create a combined form that has the best of both their powers. The story could detail their journey of learning to work together and master this new form.
In a Naruto EMS Rinnegan One Piece fanfiction, perhaps there is a mysterious island in the One Piece world that is actually a portal to the Naruto world. A One Piece character stumbles upon it and gains the powers of the EMS and Rinnegan. This character then has to learn how to control these new powers while still maintaining their own identity from the One Piece world. They could use the EMS to enhance their observation skills, like a more advanced form of Kenbunshoku Haki, and the Rinnegan to perform powerful jutsu-like attacks that are completely new to the One Piece universe.
A simple way is to make Naruto encounter an orange - themed Pokemon event. For example, a festival in the Pokemon world that features orange - colored Pokemon like Flareon. Naruto gets involved in the festivities and through that, he meets new friends and gets into some light - hearted adventures.
One interesting crossover could be a story where Naruto characters have to team up with pirates to fight a common assassin threat. For example, Naruto's ninjutsu skills combined with the pirates' sailing and combat abilities on the high seas would make for an exciting adventure. They could use their unique powers to outwit the assassins who are after a powerful treasure that has both ninja and pirate significance.