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.
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.
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 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.
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.
Sakura could play a crucial role. She might use her medical ninjutsu to heal Naruto during the fight, allowing him to keep going when he's on the verge of exhaustion. This way, Naruto can continue to face Madara with full strength.
The moment when Naruto first unleashes his new ultimate attack against Madara would be really exciting. Maybe it's a combination of his Rasengan and some kind of Sage power that creates a huge explosion of energy that Madara has to struggle to defend against.
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.
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.
One of the most exciting scenes could be when Naruto first unleashes his Nine - Tails chakra in a full - blown rage. The red chakra would surround him, his eyes would turn into slits, and he would let out a powerful roar. As he charges into the army, the soldiers would be both terrified and in awe of his power.