Well, perhaps they travel back in time to the era when the ninja clans were first forming. Their fused presence could disrupt the power balance among the clans. The fused entity might try to introduce new ninja techniques or ways of thinking based on what Naruto and Madara know from their respective times. They could also encounter their own ancestors and have to deal with the moral dilemma of interfering with their family lines. Maybe they end up influencing the creation of certain ninja villages in ways that are different from the original history.
The combination of Naruto and Madara's abilities would bring about a significant shift in the power balance of the world they time travel to. Naruto's positive influence and ability to inspire others, combined with Madara's strategic mind and combat skills, could lead to a new era of peace and cooperation. Their combined ninjutsu could also revolutionize the way ninjas in that time train and fight. For instance, Naruto's Rasengan combined with Madara's fire - based jutsu could create a whole new type of attack that others would try to emulate.
In such a fanfiction, Naruto's powerful chakra could be combined with Madara's Uchiha abilities in really interesting ways. Naruto might gain new Sharingan - like powers or be able to use some of Madara's signature jutsu more effectively. And their combined strength would probably make them nearly unbeatable in battle, changing the power dynamics in the Naruto universe completely.
Naruto would probably get Madara's Sharingan abilities. This could give him enhanced perception and the ability to copy jutsu more easily, like a supercharged version of his own ability. He might also gain access to Madara's Susanoo, which would be a huge boost to his combat capabilities.
One common theme is redemption. Madara, who was often seen as a villain in the original story, may get a chance to redeem himself through the time travel. Another theme is changing the past to fix the future. Since they can go back in time, they might try to prevent certain tragedies like the Uchiha massacre or the destruction caused by the Great Ninja Wars.
Power alteration is another theme. Since Naruto has knowledge from the future, he can change how power is distributed in the past. In some fics, this leads to a whole new power structure in the Naruto world. Also, the theme of friendship across time is quite popular. Naruto and Madara, who were enemies in the original story, form a bond in the time - travel scenarios. This bond can range from a grudging alliance to a deep friendship, depending on the fic.
One popular 'Naruto x Madara time travel fanfiction' is 'The Time - Twisted Bond'. It has an interesting plot where Naruto travels back in time and forms an unexpected alliance with Madara. The story is filled with intense battles and character development.
One possible plot could be Naruto, suddenly finding himself in Madara's body, tries to use his own values to change the course of history. He might prevent some of the darker events Madara was involved in, like the Uchiha massacre. He could also try to use Madara's power in a more positive way, for example, to bring about peace between the villages much earlier.
There are quite a few out there. 'Time - Twisted Fates' is another one. In this fanfic, Hashirama and Madara are both sent back in time by a strange jutsu gone wrong. It shows their struggle to deal with the knowledge they have of the future while trying not to disrupt the past too much. The descriptions of the ninja world in the past are really vivid.
Their combined abilities would likely make them the most powerful entity in the ninja world. For example, Naruto's ability to sense negative emotions and Madara's combat experience could lead to a new form of justice. They could easily defeat any rogue ninja or group that threatens the peace.