If we think about it, an S - Rank Naruto ability in a Fairy Tail fanfiction could also be something that is coveted by the villains. Let's say a dark guild wants to steal the power of Naruto's Sharingan (if a character with Sharingan was brought into the Fairy Tail world). They might think it's an S - Rank power that could help them achieve their evil goals. This would then lead to a big conflict where Fairy Tail has to protect this Naruto - based power from falling into the wrong hands.
Well, it could be incorporated as a new form of magic. A character in Fairy Tail might discover an ancient spellbook that has a similar power to Kamui. This discovery could change the power dynamics in the guild and lead to new adventures.
One way could be through a magical portal. Maybe a powerful mage in Fairy Tail accidentally creates a portal that links to the Naruto universe and Madara somehow gets sucked through it. Then he could use his powerful jutsu in the Fairy Tail world, creating all sorts of chaos and new storylines.
Well, it could be that a character from Fairy Tail somehow travels to the Naruto world and acquires the Rinnegan. Then, when they return to their own world, they have to adapt it to the magic - based system. They might find that the Rinnegan's abilities interact strangely with their own magic, creating new and unexpected effects.
In a Fairy Tail fanfiction, the Wood Release could be a lost magic. A character, perhaps a descendant of a long - lost civilization, discovers they have the ability to use Wood Release. They could use it to protect their guild or to fight against dark mages. The Wood Release could be used to create barriers made of thick, impenetrable wood or to trap enemies in a forest of magically - grown trees.
In a WW2 fanfiction, Fairy Tail's magic could also be used for strategic purposes. For example, if a side has access to Fairy Tail mages, they could use their teleportation magic (if any character has such magic) to quickly move troops or supplies. Also, the magic could be used to counter the new and dangerous weapons of WW2. If the enemy has developed some kind of super - weapon, the Fairy Tail mages could use their unique magics to neutralize it. However, this would also bring up moral questions within the fanfiction about the use of magic in a real - world - like war scenario.
The writer could focus on the similarities in the themes. Both Naruto and Fairy Tail have friendship as a major theme. So, a fanfiction could start with a Naruto character who values friendship in a similar way as Fairy Tail characters. They could meet and form a bond based on this shared value. Also, using side characters from both series could be easier than main characters. For instance, some of the less prominent ninja from Naruto could interact with Fairy Tail's secondary characters more smoothly.
One way could be through a crossover spell. Maybe a powerful mage in Fairy Tail accidentally creates a portal that brings Vegito into their world. Then Vegito's incredible power would be a huge shock to the Fairy Tail guild, and he could either be an ally or a misunderstood foe at first.
They could be incorporated as a new threat that the guild has to face. Maybe a dark wizard has unleashed a horde of boggarts on Magnolia, and the Fairy Tail members have to use their unique magic to defeat them.
Well, Naruto's abilities are based on chakra manipulation, while Fairy Tail mages use magic. However, Naruto's ninjutsu like the shadow clone jutsu can be used for various purposes such as reconnaissance and distraction. In Fairy Tail, some mages have similar abilities but with a magical twist. Sasuke's sharingan allows him to predict movements and see through illusions, which is somewhat like a few Fairy Tail mages who have special vision - based magic. Sakura's strength is physical, but in Fairy Tail there are mages who use magic to enhance their physical abilities. Kakashi's sharingan and his wide range of jutsu give him an edge in combat, much like a powerful and experienced Fairy Tail mage.
Naruto's chakra could be seen as a form of magic in the Fairy Tail world. His ability to use Shadow Clones, for instance, could be combined with a Fairy Tail mage's illusion magic. He could create dozens of clones that are also capable of casting illusions, confusing enemies. His Rasengan could be enhanced with different types of magic, like wind magic to make it even more powerful and destructive.