Another plot could be that Pain is reincarnated after his death, but without his memories. Naruto discovers him and decides to take him under his wing. As Pain slowly regains his memories, he struggles between his newfound friendship with Naruto and his old, vengeful self.
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 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.
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.
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 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.
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.
A plot could revolve around Sesshomaru being intrigued by Naruto's determination. Sesshomaru decides to train Naruto in some of his own combat techniques, which Naruto adapts to his own fighting style. In return, Naruto shows Sesshomaru the value of friendship and loyalty within a village. This could lead to Sesshomaru having a change of heart about his own solitary ways. Also, they could team up to face a common foe from Sesshomaru's world that has somehow entered the Naruto universe.
One idea could be that Naruto and Kashuina meet during a mission outside of Konoha. They start off as rivals, constantly trying to outdo each other in combat skills. But as they face various challenges together, they gradually develop a mutual respect and then deeper feelings. Another plot could be set in a post - war scenario where Naruto, now a hero, meets Kashuina who has a unique ability to heal the psychological scars of the war - torn ninjas. Their interaction then leads to a romantic relationship. And a third idea is that they are both students under a new sensei who pairs them up for special training. During this training, they discover things about each other that they never knew before and fall in love.
One idea could be Naruto being sent to the world of Death Note. He could use his ninja skills to try and outwit Light Yagami. Maybe he would initially be confused by the Death Note's power but then use his determination to stop Light from his killing spree. Another plot could involve Naruto meeting the Shinigami. He might learn about the balance between life and death in this new context and try to find a way to bring some of his ninja world's values to this strange new world.
Perhaps Naruto and Lala meet during a mission where Naruto is sent to a different dimension. Lala, being from an alien world, is intrigued by Naruto's determination and they form an alliance to face a common enemy in that dimension. Their different powers and abilities complement each other, and as they work together, they start to develop feelings for each other.