One plot that I find fascinating is when a dark force is threatening both the Naruto world and the Tokyo Ghoul world simultaneously. Naruto and Kaneki are the only ones aware of this threat at first. They have to travel between the two worlds, gathering allies and learning about each other's cultures and abilities along the way. This plot allows for a deep exploration of both universes and the characters within them. It's not just about the action but also about the relationships that form between the characters from different worlds.
Another idea is that Kaneki is brought to the Naruto world by Orochimaru. Orochimaru, being interested in Kaneki's unique physiology, wants to study him. Kaneki has to escape from Orochimaru's clutches and teams up with Naruto and his friends. Along the way, they discover that there are some dark secrets in the Naruto world that are related to Kaneki's past in a strange, unexpected way.
There's a plot where the Akatsuki from Naruto are interested in the advanced technology of Overwatch. They start to steal and adapt it for their own purposes. This leads to a series of clashes between the Akatsuki and the Overwatch heroes. The fanfic is full of intrigue as both sides try to outwit each other.
One interesting plot is when the Kyuubi can communicate with Naruto's friends in a 'Fox Naruto Kyuubi' fanfiction. It creates a whole new dynamic as the friends have to deal with the powerful and often grumpy Kyuubi. Another plot is the Kyuubi being able to take a physical form outside of Naruto and having its own adventures while still being linked to Naruto. It's really cool to see the Kyuubi interact with the ninja world on its own terms.
One interesting plot in Naruto Armament Haki fanfiction is that the Akatsuki organization somehow gets hold of the knowledge of Armament Haki and starts to train their members in it. This completely changes their power levels and their goals. For example, Pain could use Armament Haki to make his attacks even more devastating. Meanwhile, the Leaf Village has to scramble to understand this new ability and find a way to defend against it. There could also be a plot where a young, unknown ninja has a natural affinity for Armament Haki and is hunted by various factions who want to use his power for their own ends.
One possible scenario in a Naruto - Kaneki fanfiction could be that Kaneki somehow ends up in the Naruto world. Maybe through a strange portal or some sort of jutsu gone wrong. He might initially struggle to adapt to the different environment and the presence of chakra. But his own unique kagune abilities could be seen as a strange new form of power in the Naruto universe.
A plot where the past and future ninja teams have to compete in a tournament. Each team has their own set of skills and strategies based on their time periods. The past teams might rely more on brute force and basic jutsu, while the future teams have more advanced and unique jutsu. It would be a great opportunity to see the evolution of ninja techniques and how the different generations interact.
One interesting plot could be that Naruto's mom was secretly researching ways to communicate with the Kyuubi long before Naruto was born. Maybe she was trying to find a way to make peace with it. Another could be that she had a prophetic dream about Naruto's connection to the Kyuubi and was trying to prepare for it in her own way. For example, she might have left behind hidden messages or techniques for Naruto to discover later that would help him better control the Kyuubi's power.
One more great plot could be Naruto being trained by Edward in alchemy. Edward is a brilliant alchemist despite his young age. Naruto, with his eagerness to learn new things, would soak up all the knowledge. He could start creating his own alchemical ninja tools. For example, he could make a kunai that can transmute into different forms depending on the situation. And as he gets better at alchemy, he might start to question his own ninja way. Is it really all that different from alchemy? This internal struggle could add a lot of depth to the fanfiction.
The most interesting plots can vary. There are those that focus on the relationships between characters during the war. For instance, a fanfiction might explore the friendship between two characters who are on opposite sides. They have to make difficult choices between loyalty to their village and their friendship. Another plot could be about a prophecy that no one fully understands until the middle of the war. This prophecy ends up guiding the actions of some characters. Also, some fanfictions play with the idea of alternate dimensions opening during the war, bringing in new threats and allies from different realms.
One interesting plot could be Naruto having to prove himself in Fairy Tail's guild. Since he's from a different world with different powers, the members might be skeptical. He'd have to show that his ninja skills are just as valuable as their magic. Another plot could be him finding a way to combine his chakra with magic. It would be really cool to see how he uses this new power to fight against common enemies.