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 For example, he could become withdrawn and isolate himself from his friends.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.
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.
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.
Another aspect is the pain of betrayal. In some fanfictions, a child character might trust someone who later turns against them. This can cause deep emotional pain. The writer may describe the child's confusion, anger, and the resulting change in their personality as they deal with this kind of pain.
In the fanfiction, Naruto could be put in situations where he has to make difficult choices because of Pain's actions. For instance, he might have to decide between saving a group of villagers or going after Pain directly. This would force him to prioritize and re - evaluate his values. As he makes these tough decisions, his character would develop, becoming more decisive and strategic while still holding onto his core values of protecting others and seeking peace.
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.
One common source is discrimination. In the Naruto universe, there are different clans and some might look down on others. A child from a less - favored clan could face bullying and feel pain from this unfair treatment.