It's hard to say for sure. If the fanfiction focuses on Hinata's growth, she could potentially defeat Pain through her own skills and some unexpected twists. But Naruto is also likely to be a major factor, so it could be a combined effort of both of them that overcomes Pain.
In this fanfiction, Naruto might be extremely enraged seeing Hinata in danger against Pain. Hinata, on the other hand, would likely show her newfound strength and determination. Maybe she'd manage to land a few surprise attacks on Pain before Naruto fully jumps into the fray.
The outcome in this fanfiction could be a draw. Naruto and Hinata would put up a great fight against Pain. Naruto would be all fired up, using his Rasengan and other ninjutsu. Hinata would be there, protecting Naruto's blind spots with her gentle fist techniques. But Pain is no pushover. His ability to control gravity and rain down destruction could keep Naruto and Hinata at bay, leading to a situation where neither side can fully defeat the other.
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.
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.
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.
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.