In many fanfictions, Naruto might use new jutsus or a deeper understanding of his own power. Maybe he taps into a more powerful form of the Nine - Tails' chakra and combines it with his Sage Mode in a unique way to overpower Pain.
In some fanfictions, Naruto's pain might manifest through his actions. For example, he could become withdrawn and isolate himself from his friends. This is because Naruto has always been a social person, so any deviation from his normal behavior could be a sign of his internal pain.
One possible cause could be his sense of failure. Naruto always wants to protect his friends and village, so if he fails in a mission or is unable to save someone, it can cause him great pain.
His fighting style could become more aggressive. Without the fear of pain, he might be willing to use more extreme techniques that would otherwise be too dangerous because of the pain they cause to the user. He could push his body to the limit more often.
Konan could be really interesting. In some fanfictions, she might have a different backstory or motivation that affects the Naruto vs Pain fight. For example, she could be secretly trying to stop Pain from going too far in his destruction of the Leaf Village.
Jiraiya could be a great addition. Since he was Pain's teacher, his presence could add a lot of depth to the story. He could offer insights into Pain's past and also help Naruto understand Pain better.
It could be an old sage or a hermit who has been watching Naruto from afar. They might decide that the time is right to reveal the secret to Naruto himself or to those around him for the greater good of the ninja world.
Maybe Itachi. Since he was also part of the Anbu, and his true motives and actions while in the Anbu could be a major focus. His complex relationship with the village and his role in the Uchiha massacre could be tied to the Anbu revelations in the fanfic.
He could feel it through a shared chakra link. Since they are related and Minato sealed the Nine - Tails in Naruto, there might be a latent connection that gets activated in the fanfiction, allowing him to sense Naruto's pain on a physical and emotional level.
One reason could be some sort of special jutsu or power - up. Maybe he got a new form or ability that suppresses pain. For example, it could be related to his Sage Mode or something new entirely.