Another idea is that the nanites come from an alien source. They land in the Naruto world and start interacting with the ninja. Some ninjas might befriend the nanites, while others see them as a threat. This could lead to a whole new dynamic in the ninja world, with different factions forming based on their stance towards the nanites.
Another concept could be that the nanites are a new form of magical creature. They could have their own language and culture, and wizards and witches would have to learn how to communicate with them in order to use their powers.
Well, in Mass Effect Nanites Fanfiction, the idea of nanites being used for terraforming is quite cool. Imagine nanites being sent to a desolate planet and gradually transforming it into a habitable world. Also, the concept of nanites forming symbiotic relationships with characters. They could be like an extra 'power - up' for the characters, helping them in combat or in diplomatic situations by providing extra information or abilities.
If Naruto were to have nanites in fanfiction, it would change his character dynamics a great deal. The nanites could potentially introduce new powers that Naruto has never had before. For example, they could allow him to communicate wirelessly with his allies over long distances, or even give him the ability to hack into enemy systems if there are such things in the Naruto universe. Moreover, the nanites could be used to store and transfer chakra, which could revolutionize how Naruto uses his energy. This would open up a whole new realm of possibilities for his character development and the plot of the fanfiction as a whole.
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.
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.