Sure. There's a fanfiction where Naruto's Mokuton ability is actually a key to unlock a hidden dimension filled with ancient tree - like beings. In this dimension, Naruto has to prove himself worthy to these beings in order to fully control his Mokuton and bring back knowledge and power to the Hidden Leaf. It's a really unique plot as it combines the concept of Mokuton with a whole new world exploration.
A great Mokuton Naruto fanfiction with a unique plot is the one where Naruto's Mokuton is a result of a long - lost bloodline from a forgotten clan. The story then follows Naruto as he tries to find out more about this clan and their connection to the Mokuton. Along the way, he discovers secrets about the history of the ninja world that were long buried. This plot is different from the usual ones as it delves deep into Naruto's heritage and the mystery behind the Mokuton.
A character with both Mokuton and Sharingan would be unique in terms of combat style. They could use the Sharingan to predict an opponent's moves and then quickly use the Mokuton to create barriers or offensive wooden constructs. For example, they could see an incoming attack with the Sharingan and immediately grow a wall of thick trees with the Mokuton to block it.
One popular Naruto Mokuton Harem fanfiction is 'The Mokuton's Legacy'. It has an interesting plot where the main character with Mokuton abilities forms a harem of unique characters. Another is 'Mokuton's Ascent' which focuses on the growth of the character's Mokuton powers while also developing relationships within the harem.
Sure. There's a fanfiction where Naruto adopts a jinchuriki child from another village. This plot is unique because it delves into the relationship between two jinchuriki - Naruto, who has experienced so much as a jinchuriki himself, and this new child. He has to not only protect the child from those who would seek to use their power but also help the child come to terms with being a jinchuriki, which is a really interesting take on the Naruto universe.
A great Naruto Maki fanfiction with a unique plot is one where Maki has the ability to communicate with animals in a way that Naruto can't. They go on a mission together in a forest where they need to find a lost scroll. Maki's animal communication skills help them track down the scroll faster as the animals lead them to the location. It's a fresh take on how their skills can complement each other.
There's a fanfic called 'Seal Master Naruto'. In this one, Naruto has an unexpected encounter with an old sage who teaches him about a new form of seal that can manipulate energy in ways never seen before. The plot gets interesting as Naruto has to keep this new knowledge a secret from some of his friends who might be corrupted by its power. It's a really unique take on the Naruto Seals concept as it dives deep into the power and mystery of the seals.
Sure. There's a fanfiction where Groudon is summoned by a rogue ninja who wants to use its power to take over the ninja villages. Naruto discovers this and has to figure out how to stop the rogue ninja and send Groudon back. The unique part is that Naruto has to use his knowledge of both the ninja world and some ancient legends about Groudon that he stumbles upon.
Sure. There's a fanfiction where Obito is actually reborn as Naruto's twin brother. It's a really unique take as they grow up together, and Obito has all his past memories. This changes the dynamic of the whole Naruto story as Obito now has a second chance at life and is trying to make things right from the start with Naruto by his side.
Sure. There's one where Lee loses his ability to use taijutsu temporarily. Naruto helps him by sharing some of his chakra in an experimental way. This gives Lee a new kind of power that combines his taijutsu style with Naruto's chakra flow. It's really unique as it shows a different side of their friendship and how they can help each other in unexpected ways.
Yes, there might be one where Satan sends Naruto on a quest to retrieve a powerful dark artifact. The catch is that this artifact was once used to seal away an evil that could destroy the world if released. Naruto has to navigate through various challenges and also face the distrust of his own village as he is seen consorting with Satan.
Sure. There's a fanfiction where Naruto and Sakura get transported to a different dimension. In this dimension, the rules of chakra are different and they have to figure out how to get back home while also dealing with the local threats. It has a really unique take on their characters and their abilities.