A really interesting 'Naruto is Pain' fanfiction is the one where Naruto is transported to a parallel dimension where he is Pain. He has to live Pain's life and make the same decisions Pain did. This fanfiction is fascinating as it forces Naruto to understand Pain's motives from the inside. He has to grapple with the moral dilemmas that Pain faced, which makes for a very engaging plot.
A great plot twist might be that some of the villagers who were thought to be innocent are actually in cahoots with Pain. They could have been secretly helping him all along, providing information or weakening Konoha's defenses from the inside. This would shatter Naruto's perception of the village and add a lot of drama and conflict to the story as he has to deal with both external and internal enemies.
One plot idea could be Naruto trying to understand Pain's ideology on a deeper level while in the midst of battle. Maybe he discovers some similarities between their motives, like their desire for peace in their own ways. Another could be Naruto getting trapped in one of Pain's jutsu and having to experience Pain's past traumas first - hand, which changes his perspective on him.
Maybe in the fanfiction, Naruto loses his chakra early on in the fight against Pain. But then he discovers a hidden power within himself that is not related to chakra, like a spiritual power from his Uzumaki heritage, which he uses to turn the tables on Pain.
One idea could be Naruto focusing on rebuilding Konoha and establishing new alliances. He might use his newfound influence after defeating Pain to promote peace among the hidden villages. For example, he could start an exchange program for young ninjas to understand each other better.
Maybe in the fanfiction, Naruto could somehow enter Pain's past through a special jutsu. By seeing Pain's tragic experiences firsthand, Naruto tries to change his view on the world and prevent him from becoming the villain he is in the original story. This would involve a lot of emotional exchanges and growth for both characters.
Another plot twist might be that Pain has a hidden motive for attacking Konoha that is completely different from what was originally thought. And Naruto, in the process of defeating him, uncovers this truth. For example, Pain could be under the control of a more powerful enemy who wants to test Konoha's defenses through Pain's attack, and Naruto has to deal with this new revelation as well as defeat Pain.
One possible plot twist could be that Hinata discovers a new power within herself during the fight against Pain. Maybe she can tap into some ancient Hyuga ability that even she didn't know existed. This new power could turn the tide of the battle and surprise both Naruto and Pain.
I'd recommend 'Demonic Naruto: The Abyss Within'. The plot here is that Naruto discovers a hidden power within himself that has a demonic origin. As he explores this power, he uncovers secrets about his past and the true nature of the ninja world. It's full of twists and turns that keep you hooked from start to finish.
Sure. There's a fanfiction where Naruto is cursed by an ancient being to be silent. But this curse also gives him a unique ability to sense danger more acutely. He has to use this new ability to protect the village from a hidden threat.
One idea could be exploring the backstories of each of the Six Paths of Pain in more detail. Maybe show how Nagato came to choose them and what their lives were like before being made into his powerful tools. Another plot could be a scenario where a character tries to redeem the Six Paths of Pain instead of simply fighting them. This could involve a deep understanding of their pain and the reasons behind Nagato's actions.