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.
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 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.
In a Naruto fanfiction where he fights an army alone, he could win through his vast array of jutsu. His Shadow Clone Jutsu could be used to create multiple decoys, confusing the enemy. Also, his Rasengan, a powerful and concentrated chakra attack, could take out many foes at once. His Nine - Tails chakra might also give him a huge boost in power and endurance, allowing him to keep fighting against overwhelming odds.
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.
Well, in this kind of fanfiction, Peter is likely portrayed as a lone hero. He might be facing all sorts of challenges on his own while fighting crime. Maybe he doesn't trust the authorities or his usual allies for some reason, so he decides to take matters into his own hands. It could be a really interesting take on the character, showing his independent and determined side.
It could be a new dark wizard who is more powerful and cunning than Voldemort. This wizard might have been in hiding all this time, biding his time to take over the wizarding world. With Harry being alone, he would pose a great threat as Harry doesn't have his friends to support him in this fight.