One way could be through a magical portal. Maybe some Fairy Tail magic creates a portal that sucks Naruto and his ninja friends into the Fairy Tail world. Then they have to team up with the Fairy Tail mages to face a common enemy.
Perhaps a powerful ancient artifact exists that has the power to bridge the two universes. The characters from both Naruto and Fairy Tail are on a quest to find this artifact. Along the way, they meet and start to cooperate. The ninjas can offer their stealth and combat skills, while the Fairy Tail mages contribute their magic. This would make for an exciting and unique fanfiction.
In the fanfiction, it could be that a powerful villain has the ability to manipulate both ninja and magic powers. This forces Naruto and the Fairy Tail characters to come together. For example, they might need to combine Naruto's Rasengan with a Fairy Tail spell to defeat this strong foe. Also, they could learn from each other's fighting styles and values, like Naruto's never - give - up attitude inspiring the Fairy Tail members and vice versa.
One way could be through a crossover spell or device. For example, in fanfiction, a powerful mage from Fairy Tail might accidentally create a portal that leads to the Naruto universe while trying to perform a complex teleportation spell. The White Dragon could then find itself in the Naruto world, leading to all sorts of interesting interactions. Maybe the White Dragon's power is mistaken for a new type of chakra - based ability, and the ninja start to study it.
One way is through character crossovers. For example, a Pokemon trainer could end up in the Fairy Tail world and use their Pokemon to help in quests. They might use a Water - type Pokemon like Squirtle to put out fires during a mission. Another way is to combine the magic systems. Maybe Fairy Tail magic could be used to enhance a Pokemon's abilities, like using Fire Dragon Slayer magic on a Charmander to make its flames even hotter.
One way could be through a magical portal or rift that causes the magic from both universes to mix. For example, Natsu's fire magic could be affected by the dark and mysterious magic of the Black Bird world, making his flames have new properties. Maybe they turn purple or have the ability to nullify certain types of magic from the Black Bird world.
Well, often in such fanfictions, the Rinnegan is used as a sort of bridge between the Naruto and Fairy Tail universes. It might give a character the ability to travel between the two worlds. And when it comes to combat, the Rinnegan user could analyze the magic in Fairy Tail like they analyze chakra in Naruto. They could then use this knowledge to counter magic attacks more effectively. Also, the power of the Rinnegan could be enhanced by Fairy Tail's magic, making the character even more powerful than in the original Naruto series.
Another aspect could be the fusion of their worlds' elements. In Mortal Kombat, there are dark and hellish realms, while Naruto has its own unique elemental chakra system. A fanfiction could explore what would happen if the dark magic from Mortal Kombat's realms seeped into the Naruto universe and affected the chakra. Maybe it could create new types of jutsu or even corrupt some of the ninja. It would be a great source of conflict and adventure in the story.
Maybe a character from the Naruto universe, like Naruto himself, could be summoned to Wakanda due to some powerful magic or technology gone wrong. He would bring his ninja skills and values, and his presence could disrupt the power balance in Wakanda. This would lead to various interesting scenarios, such as Naruto learning about Wakandan culture and the Wakandans learning about ninja techniques.
It could be Naruto himself. With his already powerful ninjutsu and the potential to gain Fairy Tail magic, he would be extremely formidable. His ability to quickly learn new skills and his large chakra reserve, combined with something like Fairy Tail's celestial magic, would make him a force to be reckoned with.
Well, in fanfiction, you could have a plot where the chakra system from Naruto is somehow related to the chi in Kung Fu Panda. Maybe a character discovers that the two are different manifestations of the same energy source. This could lead to some really interesting interactions. For instance, Po could teach Naruto how to better understand and use his inner energy in a more 'Kung Fu' way, and Naruto could show Po some ninja tricks based on chakra control.
Well, a possible combination could be that the godlike powers of Naruto are somehow related to the strange anomalies in Gravity Falls. The energy that gives Naruto his power could be the same type of energy that causes the strange happenings in Gravity Falls. So, a fanfiction could explore how Naruto's power affects the balance of Gravity Falls and vice versa. He could use his chakra to control the weird forces at work in Gravity Falls.
One way to combine them creatively is through a crossover story. For example, Naruto could be transported to the Fairy Tail world and his Kyuubi powers could be mistaken for some kind of powerful magic. The characters from Fairy Tail might initially be cautious or even hostile towards Naruto because of his unknown and powerful abilities. But as the story progresses, they could learn to work together and Naruto could teach them about his world and his ninja skills while also learning about magic from the Fairy Tail mages.