Often, in these fanfictions, Naruto is confronted by his family regarding his choices. For instance, his father might not approve of his way of handling the Akatsuki threat. Or his mother could be disappointed in how he's treating his friends at a certain point. There could also be a situation where Naruto's family from a crossover world comes to take him away from Konoha because they think it's too dangerous for him there.
A typical storyline is when Naruto meets his family from a different timeline or dimension in a crossover. They might be shocked at how different he is from the Naruto in their world. Maybe his family in the fanfic has different values or powers, and they clash with Naruto over how he should use his own power or how he should lead his life.
Naruto would probably be very confused at first. He has grown up without his parents, so suddenly being confronted by them or a new family in a crossover would be a huge shock. He might be hesitant to trust them right away.
One creative storyline could be that Naruto and Megaman team up to fight a new enemy that has the ability to steal both ninjutsu and robot powers. They would have to combine their unique skills to defeat this powerful foe.
Another could be a time - travel scenario where Naruto goes back in time and meets Rikudou Sennin. They then team up to prevent a great evil from ever arising in the first place. This would allow for a lot of character development and exploration of the Naruto universe's history.
One interesting storyline could be where Naruto characters are teleported to the world of Zelda. Naruto, with his determination and never - give - up attitude, might take on the role of a hero in the Zelda world. He could use his shadow clones to solve puzzles or fight off hordes of Bokoblins. Another could be Link getting the ability to use chakra, which would completely change the way he battles enemies. He could use ninjutsu techniques along with his swordsmanship, creating a unique combat style.
One interesting storyline could be Naruto using the Sharingan to enhance his combat skills in a new and unexpected way. For example, he might combine his Rasengan with Sharingan - powered genjutsu to create a more powerful and deceptive attack.
A really cool storyline in a Naruto - DC crossover fanfiction could be the idea of Naruto characters training DC heroes in the ways of chakra. Superman, for example, could learn to control chakra and use it to enhance his already superhuman abilities. Or, a story where the Justice League has to deal with the political intrigue of the Hidden Villages in Naruto's world. It would be a clash of two very different political systems. Also, a storyline where a Naruto character like Sasuke becomes a sort of anti - hero in the DC Universe, causing chaos among the heroes and villains alike could be fascinating.
One possible storyline is a cross - over where the ninjas in Naruto are exposed to the equivalent exchange principle of alchemy. They might start using it in their training, like instead of just relying on chakra, they think about what they are giving up to gain a new skill. For instance, a ninja might give up some of his speed to gain more strength. In the case of the Fullmetal Alchemist characters in the Naruto world, they could be involved in the battles between the villages. Alphonse could use his armor body to protect the villagers from attacks. And Scar from Fullmetal Alchemist could have an interesting interaction with the shinobi, as his unique form of alchemy might be seen as a very different type of jutsu.
Well, there could be a story where the Nine - Tailed Fox's power gets unleashed in the Mount and Blade world. This would cause chaos among the kingdoms and factions. The Mount and Blade characters would have to figure out how to deal with this powerful and unknown force. At the same time, Naruto would be in a struggle to control the Nine - Tails' power in this new and unfamiliar setting.
One interesting storyline could be the combination of Naruto's ninjutsu with Final Fantasy 7's materia system. Imagine Naruto using materia - enhanced jutsus. Another could be Cloud and Naruto teaming up to fight a common enemy like Sephiroth and Madara combined. It would be epic to see their different fighting styles blend.
One possible interesting storyline could be a female Naruto ending up in the Bleach universe and learning about the different spiritual powers there. She might try to adapt her ninja skills to the new environment filled with Hollows and Soul Reapers. Another could be a Bleach character getting transported to the Naruto world and being amazed by the chakra system. For example, Ichigo might be curious about how chakra is different from his reiatsu.