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 a 'Harry Fights Alone' fanfiction, the plot could involve Harry being betrayed by his friends. Maybe they are put under a spell that makes them turn against him. Harry then has to face the dark forces all by himself. He might have to rely on his own wits and the few spells he has mastered alone. For example, he could be in a situation where he has to battle Voldemort's minions without Ron and Hermione to back him up, and he discovers new powers within himself during this struggle.
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.
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.
One possible plot could be that Naruto is somehow transported to a different timeline where he has to fight the Hokage for a misunderstanding. Maybe there's a villain who has manipulated events to make the Hokage think Naruto is a threat. So Naruto has to fight not only to prove his innocence but also to save the village from the real danger that the villain poses.
Well, one possibility could be that Naruto uses his shadow clone jutsu to confuse the Humunculi. Since they are used to a more straightforward combat style, the clones might throw them off. Naruto could then use his Rasengan to directly attack them. Maybe he would also team up with some of the characters from the FMA world who oppose the Humunculi.
One possible plot could be that Zeref has a new target in the Naruto universe. Naruto discovers this and decides to confront him. At first, Naruto is outmatched as he doesn't understand Zeref's magic. But then he starts to analyze it during their battles and figures out ways to counter it. Meanwhile, Zeref is intrigued by Naruto's never - say - die attitude and chakra. The plot could also involve other characters from both universes getting involved, either to help or to cause more chaos.
Well, the plot could involve Naruto being in a post - apocalyptic world filled with zombies. His ninja skills would be put to the extreme test. He could team up with his friends like Sasuke and Sakura. Naruto would have to adapt his fighting style as zombies don't feel pain like normal foes. He might use his speed and agility to dodge the zombies and then use his powerful ninjutsu to take them out in groups.
It could also be a sparring session gone wrong. Naruto might be training with the Konoha 12, but his new and powerful techniques are too intense. This causes the others to feel threatened and they end up in a full - on fight. Naruto would then have to control his power and show his friends that he doesn't mean to harm them.