Some fanfictions focus on Naruto having a different upbringing. For instance, if he was raised by a different clan, like the Hyuga. This would give him access to their unique abilities and fighting styles. He could also have a different set of friends and rivals, which would completely reshape his character development and the overall plot of the story.
Another great storyline could be about a character from Naruto ending up in the world of The Legend of Korra and having to adapt. Maybe Sasuke somehow gets transported there and has to learn about the new bending techniques and how to fit into this different society. He could end up sharing his ninja skills with the benders and creating a whole new form of combat.
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 about a young owl in the Legend of the Guardians world who discovers a hidden power within itself. Maybe it's the ability to communicate with other animals in a unique way, which then leads it on a journey to find out more about this power and how it can use it to protect the owl kingdom.
One interesting storyline could be Emrys' journey to discover his true powers. Maybe he starts off as an ordinary person but then gradually realizes he has some extraordinary abilities that are tied to his heritage.
One interesting storyline could be a crossover where Naruto's world of ninjas collides with Seras' vampiric world. Maybe Naruto is on a mission in a strange land and stumbles upon Seras. They could team up to fight a common enemy that threatens both their worlds.
Well, in some Naruto sickle fanfiction, there might be a plot where the sickle is a cursed weapon. It might bring misfortune to whoever wields it, but the main character has to find a way to break the curse. Maybe it was used in a past war and has a dark history. Also, a story could revolve around a young ninja who inherits a sickle from a fallen hero and has to live up to the legacy while also uncovering the secrets of the sickle.
One interesting storyline could be a ninja who discovers a pair of magical headphones in the Naruto world. These headphones might enhance their chakra control when they wear them while training. For example, they could hear the natural flow of chakra in the environment, like the rustling of leaves representing wind chakra or the gurgling of a stream for water chakra.
Another storyline could involve Naruto's daughter being sent on a special mission that is related to a mystery from Naruto's past. Maybe she discovers some secrets about her father's early days that were never known before. This could lead to her having to make some tough decisions about how to handle this newfound knowledge.
One interesting storyline could be a crossover where Naruto's world of ninjas meets Seryu's world. Maybe Naruto's team is on a mission in Seryu's land and they have to team up with her to fight a common enemy. Another could be a story where Seryu, with her strong sense of justice, is somehow transported to the Naruto universe and has to learn the ways of the ninja while also trying to uphold her own values. There could also be a fanfic where Naruto and Seryu become friends and Naruto tries to show Seryu a different perspective on justice, as his concept of it might be more forgiving compared to hers.
One interesting storyline could be about Naruto having a new and powerful jutsu that he discovers in a flash of inspiration. This jutsu might be related to his chakra nature in a unique way. Another could be a fanfiction where Naruto travels back in time in a flash of some mysterious power and has to relive parts of his past with his new knowledge. There could also be a story where Naruto meets a new character who has a special connection to the flashy, yet dangerous, forbidden jutsus.