A third idea is that Naruto starts training a new generation of ninjas in a different way. Instead of just focusing on combat skills, he emphasizes on moral values and understanding the true meaning of being a ninja. He could tell his own experiences, including his encounter with Pain, as lessons for the young ones.
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.
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 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.
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.
One idea could be exploring a different backstory for Pain. Maybe he had a secret friendship with a Konoha ninja before turning to his dark path. This could add a new layer of complexity to his character and the conflict in the arc.
In this type of fanfiction, there could be a plot where a strange disease starts affecting ninjas' chakra systems. Naruto has to lead the search for a cure, which takes him on a journey across the ninja world. Along the way, he discovers secrets about the origin of chakra that were long forgotten. This could also lead to some interesting character development for other supporting characters as they face this new crisis together.
One plot idea could be that Naruto and Ino team up in a unique way during the Pain Invasion. Ino could use her mind - transfer jutsu to assist Naruto in predicting Pain's attacks. For example, she might be able to get inside the minds of Pain's summoned creatures and relay information to Naruto, giving him an edge in battle.
One plot idea could be that Pain, after realizing Hinata's strong will during their encounter in the original story, becomes intrigued by her. He starts to observe her from afar and eventually falls for her as he sees her kindness towards others in the Hidden Leaf Village.
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.
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.
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.