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.
One possible plot development could be that after saving Naruto, Madara tries to mentor him. He sees Naruto's potential and wants to shape him into an even greater ninja, sharing his own knowledge and skills that have been honed over years.
Well, a plot could develop where Naruto is trained in secret by an old ally of Madara and Hashirama who knows about his heritage. This training could involve unlocking ancient jutsu that were lost over time. Also, his relationships with other characters like Sakura and Kakashi would change as they try to come to terms with his new - found family background. And there could be a conflict with the Akatsuki, who might see Naruto as an even greater threat or a valuable asset because of his relation to Madara and Hashirama.
One possible plot development could be Naruto developing new and unexpected powers as a result of the experiments. For example, he might gain the ability to use some of Madara's unique jutsu in a different way. Another could be Naruto's friends trying to rescue him and in the process learning more about Madara's true motives and the nature of the experiments. Maybe Naruto also has to struggle with his own identity as he is changed by the experiments.
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.
One possible plot development could be that Naruto's new look causes confusion among his friends. They might start to question if he's still the same Naruto they know. Another is that enemies could be either more afraid or more eager to fight him, thinking he has some of Madara's power.
One possible plot development could be Naruto facing internal struggles. He has always been Naruto Uzumaki, and now with Madara's DNA, he might question his identity. Another could be that the village starts to view him differently. Some might fear his newfound power, while others might see him as a potential threat. There could also be a plot where Naruto has to learn to control the new powers that come with Madara's DNA quickly, as an enemy emerges who can only be defeated with these new abilities.
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.
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.
One possible plot development could be that Naruto is mistaken for Madara by some of the older characters who knew Madara. This could lead to some interesting confrontations and misunderstandings.
Well, the plot might develop with Sakura being hunted by ninja clans who fear the return of Madara through her. She could then go on a journey to find out more about her reincarnation status. Along the way, she might discover some long - lost jutsu that Madara was known for. She could also form an unlikely alliance with some of Madara's old comrades or enemies in the fanfic. And as she delves deeper into her new identity, she might have to make some tough choices between her old self and this new 'Madara - influenced' self.