A cool concept could be that there is a nano - virus spreading in the ninja world, and Naruto has to find a way to stop it using his unique chakra and his ability to make friends and allies. He might have to team up with some unexpected characters to combat this new threat.
One idea could be a story where Naruto discovers a hidden nano - technology in the Hidden Leaf Village that was left by an ancient shinobi. This tech gives him new powers to fight enemies.
Maybe a fanfiction where Naruto's clones are enhanced with nano - particles. These clones can then perform tasks that normal clones couldn't, like infiltrating high - tech security systems in enemy bases.
One interesting idea could be the combination of Naruto's ninja skills with mecha technology. For example, Naruto might use his chakra to power up the mecha in unique ways. Another idea could be the new enemies that are created specifically for this mecha - Naruto concept, like robotic shinobi that require different combat strategies compared to normal foes. Also, the design of the mecha Naruto itself can be really cool, perhaps with features inspired by the Nine - Tails.
One interesting plot idea could be a time - travel story. For example, Naruto is sent back in time to the era of the First Hokage. He could use his knowledge of future jutsu and events to change things for the better in the past. Another idea is a story where Naruto discovers a hidden clan within Konoha that has a unique and powerful Kekkei Genkai. He then has to help this clan gain acceptance in the village. A third idea might be a story where Naruto is turned into a different creature, like a cat or a fox, and has to find a way to turn back while still dealing with the normal threats to the village.
One idea could be that Neji discovers a new hidden power within Naruto that he helps Naruto master. This could lead to them having to face a new, powerful enemy together.
Another idea is that Aizen somehow ends up in the Naruto universe during the time of the Fourth Great Ninja War. He could try to manipulate both sides for his own gain. But Naruto, with his ability to see the good in people, might try to reason with Aizen and show him a different path. It could be a story of redemption or a great battle if Aizen refuses.
In a 'Naruto Mermaid Fanfiction', the mermaids could be in danger from an evil organization that wants to capture them for their precious scales. Naruto teams up with a mermaid princess to stop this threat and in the process, they learn about each other's worlds.
One idea could be a crossover where Naruto and Pucca end up in the same world due to a strange ninja jutsu gone wrong. Naruto is confused by Pucca's constant chasing of Garu, and he tries to help Garu escape in his own Naruto - style way.
Well, you could write a fanfiction where the Nine - Tails in Naruto has some sort of connection to a powerful entity in the Seraphim universe. This connection could lead to a series of events that require Naruto and the Seraphim characters to work together. Or perhaps a character from Seraphim is reincarnated as a ninja in the Naruto world and has to adapt to the new way of life while still having some of their Seraphim abilities.
One idea could be a blacksmith who creates unique ninja tools with special abilities that give the wielder an edge in battle. For example, a kunai that can change its shape during flight to avoid enemy defenses.
You could also write a fanfiction about Naruto being raised by a different clan in the village. For example, if he was raised by the Uchiha clan, it would have a huge impact on his character development and relationships within the village.
One idea could be that Krampus is summoned in the Naruto world during a particularly harsh winter. He mistakes the ninja villages for places full of naughty 'children' (in this case, ninjas who have misbehaved according to some warped view). Naruto then has to convince Krampus that the ninjas are actually good at heart and are just trying to protect their homes.