One idea could be Naruto going back in time and meeting his parents when they were young. He could try to prevent their early deaths or change certain events that led to the hardships in his own life. Another plot could be Naruto ending up in the time of the First Hokage, and learning the original ninja ways that were perhaps lost or changed over time. He might also have to deal with the different political situations of that era.
One plot idea could be that Naruto is a celestial being sent to the human world on a mission. He has powers far beyond what normal ninjas possess, like the ability to control the elements on a much larger scale. For example, he could stop a natural disaster by simply willing it. Another idea is that he's a spirit in a human form, and he has to find a way to return to his spirit realm while still protecting the village. This could involve him learning about his true identity through a series of mysterious encounters.
Well, a plot could involve Naruto being initially ostracized in the village because of his deafness. But then, he proves his worth by using his unique perspective. Since he can't hear, he becomes extremely observant of body language. This helps him in battles and also in understanding the true feelings of people around him. He could also form a special bond with a character who is also an outcast, perhaps someone with a disability of their own, and together they change the perception of the village towards those with differences.
A possible plot is that Naruto's blindness is a result of a powerful enemy's attack. This forces him into a new world of darkness, but also reveals hidden powers within him. He could start to see things in a different way, not literally but metaphorically. His new - found understanding could lead him to be a better leader. For instance, he might be able to understand the pain of the oppressed in a more profound way, and thus fight for their rights more vehemently. His blindness could also be a way to bring out the best in his friends, as they rally around him to support and protect him.
Another plot could be that Naruto is adopted by an older ninja who has retired from active duty. This ninja has a lot of wisdom and secrets. Under his guidance, Naruto discovers a new power within himself that was hidden all along.
A possible plot could be that both Naruto and Hashirama are reborn simultaneously. They might team up to face a new, powerful enemy that even the combined forces of the Hidden Leaf couldn't handle before. Since Naruto has his Uzumaki chakra and Hashirama has his Senju power, together they could create new and powerful jutsu. For example, Naruto's chakra could enhance Hashirama's Wood Style to cover larger areas or be more durable.
One plot idea could be Naruto using his intelligence to outwit his enemies in a more calculated and cold way. For example, instead of his usual impulsive attacks, he carefully plans each move to take down powerful foes. He might study their weaknesses in secret and then strike when they least expect it.
One plot idea could be that Naruto is seriously injured during a battle with a new, powerful enemy. His friends then have to find a rare herb or a special healer to save him. Another could be he's injured while protecting the village from a sneak attack and has to recover in secret to avoid the enemy knowing his weakened state.
Well, a possible plot is that Sakura starts getting close to an older ninja who is mentoring her in a new medical jutsu. Naruto, being jealous, starts training extra hard in medical ninjutsu too just to be around her more. He might also be jealous if Sakura shows admiration for a different village's ninja. For example, if a ninja from the Sand Village shows off some amazing skills and Sakura is impressed, Naruto would feel the need to prove that he's just as good or better.
Well, a plot could revolve around Naruto being in a situation where he has to keep a big secret from his friends, just like Itachi did. This could create a lot of internal conflict for Naruto. He might start to isolate himself, which his friends would find strange. Also, in terms of power, Naruto could be exposed to a power similar to Itachi's Mangekyo Sharingan. He would have to learn to control it without losing himself, and this could be a great arc in the fanfiction. It would show Naruto's growth as he struggles with the new power and the implications of using it.
Maybe Itachi is on a secret mission outside of Konoha and he saves Naruto from a group of rogue ninjas. Naruto, being Naruto, is immediately drawn to Itachi's strength and kindness. They start to train together in secret. As they train, Naruto discovers Itachi's past and the burden he carries. This leads to Naruto vowing to help Itachi find a way to clear his name in Konoha and they become close friends in the process.