Naruto is often paired with Madara in some fanfictions. Their interactions can be really intense, as Naruto tries to either convince Madara to change his ways or fight against his reborn form.
When Madara travels through time, he might find allies in unexpected places. For instance, some of the minor ninja clans that were oppressed by the larger clans in the past could see Madara as a liberator if he offers them a better future. On the other hand, those who benefit from the current ninja world order, such as the Daimyo or certain powerful shinobi from other villages, might see Madara as a threat and become his enemies.
Often, Naruto might be paired with Madara in some sense. Their opposing views on power and peace could create interesting interactions in the fanfiction.
Sasuke could be a main character as well. Given his own experiences of being an outcast and having a thirst for power at times, he could relate to Madara in some ways. They might form an unexpected alliance or have a rivalry based on their shared experiences of feeling neglected or misunderstood in the ninja world.
Naruto himself could still be a main character. His relationship with Madara's reincarnation could be explored, like how he tries to understand this new version of an old enemy and whether he can trust him or not.
Sasuke is often a popular character in these fanfictions. He might play a role in helping Naruto against Madara or have his own motives during their battle. Kakashi can also be a prominent figure, perhaps using his Sharingan in a crucial moment to assist Naruto. Another popular character could be Hashirama, as his connection to Madara is a key part of the original story and can be further explored in fanfiction.
Maybe an orphan from a non - Uchiha clan who has a special ability that Madara finds interesting. This character would be malleable and eager to learn from Madara, as they have no other real family or guidance. They could bring a fresh perspective to Madara's teachings.