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.
Naruto would likely gain the ability to use all six paths techniques. The Rinnegan allows the user to manipulate gravity, as seen when Madara used it. Naruto could use this to enhance his combat skills, for example, pulling enemies towards him or pushing them away forcefully. He could also use the Preta Path to absorb chakra, which would be a great addition to his already large chakra reserves.
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.
Well, he might gain the ability to create spider - like webs for trapping enemies. It could be a really cool addition to his ninja skills, allowing him to set up traps quickly and immobilize opponents.
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.
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.
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.
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.
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.