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.
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 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.
Well, perhaps in this 'naruto invasion of konoha fanfiction', Naruto is actually being mind - controlled to lead the invasion himself. It would be a huge shock for his friends and allies when they find out. This could lead to a lot of internal conflict as they try to figure out how to stop him without hurting him.
One possible plot development could be Naruto's efforts to rebuild Konoha. He might focus on strengthening the village's defenses and training new shinobi. Another could be his exploration of new jutsu, inspired by his battle with Pain. He could also work on improving relations with other villages.
He could focus on chakra control training. Since he often has issues with his Nine - Tails chakra going out of control, this would be a logical step.
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.
Naruto is, of course, very memorable. His determination to protect the village against Pain is always a central and inspiring part of any such fanfiction.
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.