A really cool plot twist could be that Naruto actually befriends one of Pain's bodies during the fight. Through their interaction, he manages to turn that body against the others. This would add a whole new dimension to the fight and the story, as it shows Naruto's ability to find common ground even with his enemies and use it to his advantage in defeating 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.
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.
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.
One possible plot twist could be that Naruto's death at Pain's hands leads to a dark turn in the Hidden Leaf. The villagers, in their grief and anger, start to question the ninja way and some might turn to darker methods of revenge. For example, Sasuke, upon hearing the news, could completely abandon any hope of redemption and go on a full - out rampage against the Akatsuki.
In some fanfics, Naruto might team up with unexpected characters to defeat Pain. For example, he could join forces with Orochimaru. Orochimaru, with his knowledge of jutsus and dark arts, and Naruto, with his brute strength and positive energy, create a unique combination that outsmarts Pain's abilities.
One interesting plot twist could be that Naruto discovers he has a hidden power from a long - lost clan that changes the course of the final battle. This power might be something that gives him an edge against a seemingly unbeatable foe.
A great plot twist could be that Naruto turns out to be a half - vampire. It would completely change his character arc and how others in the Naruto world perceive him.
A possible plot twist could be that Naruto's blindness was actually caused by an enemy's secret jutsu that was meant to be permanent, but it turns out that Naruto's Uzumaki bloodline has a hidden ability that can reverse the blindness under certain conditions. This would add an element of mystery and hope to the story.
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.