Naruto could potentially use a new form of the Nine - Tails Chakra Mode. Maybe he combines it with his Sage Mode in a more seamless way than ever before. This would give him enhanced strength, speed, and the ability to sense danger more acutely.
In such a fanfiction, Naruto could potentially win by using his new Sage of Six Paths powers to their fullest. He might be able to overpower Madara's Rinnegan abilities. For example, Naruto could use his massive chakra reserves to create countless shadow clones and overwhelm Madara in a battle of attrition.
In a 'naruto fights alone fanfiction', it could be that Naruto is on a mission in a foreign land where he has no support. The local ninjas are all against him for some reason. He has to use his Nine - Tails chakra in a more discreet way as he can't afford to go all - out and draw too much attention. He might befriend some local animals or spirits who help him in a more indirect way, like giving him information about the enemies' weaknesses.
Maybe an ancient evil ninja who was sealed away long ago but has now been released. This antagonist could have powers that nullify any communication or summoning jutsu, forcing Naruto to fight alone. He would be extremely powerful and know many forgotten and deadly jutsu.
In this fanfiction scenario, Naruto could potentially use new and untested jutsu. He might draw on the power of his nine - tailed fox in a completely different way. Maybe he'd combine Sage Mode with some secret Uzumaki clan technique he discovers during the fight.
Naruto could gain the ability to communicate telepathically using the force. This would be useful in coordinating with his teammates during a battle or getting information from afar. He might also be able to levitate himself or objects of significant size, which would be a great advantage in both combat and non - combat situations. For instance, he could levitate boulders to use as cover or to attack his enemies. Also, he could potentially use the force to heal himself or others to some extent, a very different kind of power compared to his normal ninja healing techniques.
Naruto might create a jutsu that uses his Uzumaki clan's sealing techniques along with his chakra. Maybe a sealing - Rasengan that can seal an opponent's chakra for a short time. Sasuke could come up with a jutsu that uses the power of the Rinnegan and his own lightning - style chakra to create a super - charged lightning attack that can cut through almost anything.
Well, one possible plot could be that Naruto discovers a new jutsu specifically designed to counter Madara's powerful Sharingan abilities. This jutsu might be related to the Sage of Six Paths' power that he already has. With this new power, Naruto engages in a series of intense battles with Madara, each time getting closer to figuring out Madara's weaknesses.
He might gain some of Madara's Sharingan - related abilities. Maybe he could use some of the advanced genjutsu techniques that Madara was proficient in. Since Madara had strong chakra, Naruto could also potentially have an increase in his own chakra levels or a new way to manipulate chakra, like Madara's ability to control the Susanoo.
He could develop some sort of psychic power that doesn't rely on chakra. This could be a power related to his willpower, allowing him to influence the minds of his opponents or sense their intentions from a distance.
Maybe in the fanfiction, Madara has a hidden weakness that only Naruto can sense. For example, Naruto might notice that Madara's control over his Sharingan wavers when he's near a certain type of natural energy. So Naruto uses this to his advantage and lures Madara to that area during the fight.