One common plot twist could be that Naruto, on his second chance, discovers that some of the people he thought were friends in his first life were actually secretly working against Konoha. For example, he might find out that a seemingly innocent villager was passing information to the enemy. Another plot twist could be related to his family. Maybe he uncovers new secrets about his father, like that Minato had a secret mission that was never fully completed and Naruto has to finish it in this new timeline. And sometimes, the time travel itself can be a twist. He might find out that he wasn't sent back in time by chance but by some powerful entity with its own motives, like an ancient sage who wants Naruto to change the future to avoid a great disaster that will befall the ninja world.
Naruto himself is, of course, the most popular character to feature. After all, it's his second chance at life and time travel. Sasuke is also very popular. His complex relationship with Naruto can be explored in new and interesting ways in a time - travel scenario. Kakashi is another one. His role as a mentor can be expanded upon, especially if Naruto has knowledge from the future that he can share with Kakashi. Hinata is often included as well. Her unrequited love for Naruto can be developed further, and perhaps in the time - travel plot, she can play a more important role in Naruto's life earlier on.
The theme of changing fate is also prevalent. Naruto tries to change the destinies of his friends and the whole shinobi world. He doesn't want to see the same tragedies occur again. Also, self - discovery is a theme. As he changes things, he also discovers new aspects of himself and his capabilities. He might realize he could have been a better leader earlier if he had known certain things.
In this type of fanfiction, a frequent plot is Naruto traveling back to the time when Orochimaru was still a threat. He could use his knowledge of Orochimaru's plans to stop him before he became too powerful. He might also be able to save some of Orochimaru's victims, like the people he experimented on. Another plot is Naruto going back to the time when Pain attacked the village. He could come up with a better strategy to defeat Pain and save more of the villagers. And sometimes, the plot involves Naruto using his second chance to understand the secrets of the tailed beasts earlier and form a stronger bond with Kurama.
Another one is 'Naruto's Second Chance at Life'. Here, Naruto is given a second chance and he decides to focus on training earlier and building stronger relationships. The story delves into his character development as he tries to become a better shinobi while also changing the fates of his friends. It's a really engaging read with a lot of heart.
Naruto in these fanfictions develops a different kind of confidence. Instead of the brash confidence based on his willpower in the original story, it's more a confidence born out of knowledge. He's able to plan ahead and make better decisions regarding his training. His character also becomes more diplomatic as he tries to prevent future conflicts. For instance, he might be more involved in peace talks between different ninja clans. His understanding of the shinobi world expands more quickly, and he uses this to his advantage to not only better himself but also to improve the lives of those around him.
One popular second chance time travel novel is 'Outlander' by Diana Gabaldon. It follows a World War II nurse who travels back in time to 18th - century Scotland.
One characteristic is the chance for the protagonist to correct past mistakes. For example, in 'Re:Zero', Subaru can learn from his previous failures and try to change the outcome. Another is the exploration of new worlds. Since they are time - traveling, often to a different world, like in 'The Devil is a Part - Timer!', they get to experience new cultures and magic systems. Also, character growth is a big part. They start with their old selves but through the second chance, they develop into stronger, wiser characters.
One possible plot could be that Naruto and Sasuke are given a second chance to start their relationship anew. Maybe they go back in time and are able to avoid all the conflicts that led to their estrangement. They could then focus on building a true friendship from the start, training together and sharing their dreams without the shadow of revenge or power-hunger clouding their minds.
Redemption is a common theme. Since Tony gets a second chance, he often tries to fix his past wrongs, whether it was a mistake in a relationship or a strategic error. Another theme is self - discovery. Through time travel, he gets to see different versions of himself and understand who he really is.