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.
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.
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.
If we think about it, the Sharingan in the Naruto universe has some similarities to the power of the Death Note in terms of perception. So, a character like Sasuke could potentially use his Sharingan to better understand the workings of the Death Note. He could then teach Naruto how to use it in a more strategic way. Also, the teleportation jutsu in Naruto could be used to quickly get to the location of the target whose name is about to be written in the Death Note, making the process more efficient.
One way to combine the GTA V and Naruto universes in a fanfic could be through a crossover of characters. For example, Naruto characters could be transported into the GTA V world. They might use their ninja skills in the modern, crime - filled setting of Los Santos. Naruto could use his shadow clones to perform heists in a very unique way. Sasuke could use his Sharingan to outwit the criminals and corrupt cops in the city.
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 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.
In fanfiction, they often connect through magical portals. For example, a portal could open up in the Forbidden Forest in Hogwarts and lead to Gravity Falls. This allows characters from both universes to interact.
One way to combine them could be through a crossover device. For example, a powerful Pokemon like Mewtwo could accidentally open a portal to the Avengers' universe. Then, the Avengers might mistake the Pokemon for some kind of new alien threat. They would try to contain it, but soon realize that the Pokemon has no malicious intent. Meanwhile, the Pokemon trainer who follows Mewtwo through the portal has to team up with the Avengers to find a way back home and also deal with any villains in the Avengers' world that might try to use the Pokemon for their own gain.
One way is through the power systems. The chakra in Naruto and the energy used in Street Fighter can be merged. For instance, a character could use chakra to enhance the power of a Street Fighter move like Chun - Li's Spinning Bird Kick.