Maybe Orochimaru's former followers who are still lurking in the shadows. They see Naruto as a threat and Hinata as an easy target to get to Naruto. Another possibility could be some power - hungry shinobi from other villages who view Konoha as weak after the Pain incident. They might target Naruto and Hinata as key figures in Konoha's future to try and undermine the village's rebuilding efforts.
One possible plot could be that Hinata and Naruto start to train together more intensively. After facing Pain, Naruto realizes Hinata's feelings for him more deeply. They could go on missions side by side, and Hinata becomes stronger under Naruto's influence. Naruto, in turn, starts to see Hinata as not just a friend but someone he could potentially have a future with.
Here's how a fanfic might go. After the battle with Pain, Naruto is surrounded by people, but his eyes keep searching for Hinata. When he finally spots her, he makes his way through the crowd. Hinata is blushing but stands her ground. Naruto reaches her and says, 'Thank you for always being there for me.' Then, he cups her face and kisses her. This kiss is a culmination of all the times Hinata has supported Naruto, and now he's finally realizing his own feelings for her.
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One idea could be that Sakura uses her medical ninjutsu to heal Kankuro after he gets seriously injured in a battle against a powerful enemy. She has to overcome various challenges like limited supplies and the unique nature of Kankuro's puppet - related injuries.
It could also lead to changes in the power dynamics. Without Naruto, Akatsuki might see the Hidden Leaf Village as an easier target. However, the village could also discover new heroes among the younger generation. The remaining characters would have to find new sources of inspiration and strength.
In many fanfictions, after the Pain arc, Naruto and Hinata's relationship often deepens. Naruto starts to see Hinata in a new light. He realizes her strength and her unwavering feelings for him. This can lead to more interactions between them, like Naruto becoming more protective of Hinata and Hinata being more confident in expressing her love for Naruto.
It could symbolize a new chapter in their relationship. Before, Naruto was mostly focused on his goals and being recognized in the village. But after facing Pain, he might have a new perspective on life and love. The kiss with Hinata could be the start of a deeper, more romantic connection, showing that he's ready to explore his feelings for her and let someone be close to him in a different way.
A plot twist could be that the method Sakura uses to heal Kankuro has an unexpected side effect. For example, it gives him a temporary boost in his puppet - using abilities that he has to quickly learn to control.