One idea could be that Naruto and Shikamaru travel back to the time when the Uchiha clan was still intact. They could try to prevent the massacre. Maybe Naruto uses his future knowledge of Sasuke's pain to convince the clan leaders to find a different solution.
Another plot could be that they travel to the time of the First Hokage. Naruto, being his boisterous self, might accidentally disrupt some of the early village building processes. Shikamaru, with his intelligence, has to figure out how to fix things without changing history too much. For example, they could be involved in the negotiations between the Senju and Uchiha clans that led to the formation of Konoha.
One idea could be a mission where they have to infiltrate an enemy base. Naruto's boldness, Shikamaru's strategic mind, and Shino's stealth and bug abilities would all come into play. They could face various traps and enemies within the base, and have to rely on each other's strengths to succeed.
One interesting plot idea could be that Naruto and Kishina travel back to a time when the Uchiha clan was still intact. They could try to prevent the future tragedies that are related to the Uchiha. Another idea is that they go back to a time when the Hidden Leaf Village was first founded and get to experience the early days of the village's development. They might also have to deal with different power structures and rivalries that were present at that time.
One idea could be that Naruto and Kishina travel back to the time when the Uchiha clan was at its peak. They could try to prevent the future tragedies related to the Uchiha. Another could be them going back to the era of the First Hokage and learning about the origins of Konoha and how it was built. They might also discover secrets about their own clans that were lost over time.
One interesting plot idea could be that Naruto travels back in time and meets a young Mikoto. He could end up influencing the events that led to the Uchiha massacre in some way. Maybe he tries to prevent it by changing the relationship between the Uchiha clan and the village.
Maybe they travel back to a time when a great threat was about to destroy the village but was forgotten in history. Naruto and Kyshina, with their combined strength and knowledge of future jutsu, are able to defeat the threat and rewrite history so that the village doesn't suffer the losses it originally did. This could also lead to new relationships being formed between different characters who might not have interacted in the original timeline.
One idea could be that Naruto and Tenten travel back to the founding of Konoha. They could use their modern knowledge to influence the village's early development, like introducing new training techniques. Another could be that they go back to a time when a great battle was about to start and they change the outcome, thus changing the future of the ninja world.
Well, in a Naruto x Tobirama time travel fanfiction, it could be that Naruto is sent back in time to right before Tobirama's death. Naruto, being Naruto, tries to save Tobirama. Tobirama is initially suspicious of Naruto but then realizes his good intentions. Together, they work on a plan to make the ninja world a better place even before Hashirama's time. They could come up with new ways of training ninjas, ways that are more inclusive and less likely to lead to clan rivalries. This would then change the course of the entire Naruto universe.
One plot idea could be that Mikoto travels back in time and tries to prevent certain tragedies from happening in the Naruto universe. Maybe she wants to stop the Uchiha massacre, and in the process, she forms a strong bond with Naruto, who is also involved in her efforts.
Another plot could be that both Naruto and Kaguya are sent back in time together accidentally. They end up in a time when the ninja world was just beginning. They have to work together to survive in this primitive world, and in the process, they start to understand each other better. Naruto tries to teach Kaguya about the concept of friendship and loyalty, which she has long forgotten. As they face various challenges, their relationship evolves, and they may even find a way to change the future for the better.
Maybe they travel back to a crucial moment in the Fourth Great Ninja War. With their future knowledge, they are able to prevent certain tragedies from occurring. Naruto could change the course of a battle by warning the Allied Shinobi Forces about an ambush, and Temari could use her strategic mind to better organize the troops.