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.
Yes, it could be a real story. There are many experiences in life where pain and gain are closely related. For example, athletes often endure a great deal of pain during training but gain excellent physical condition and the possibility of winning championships. However, without more context, it's hard to be completely sure if it specifically refers to a real story.
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 For example, he could become withdrawn and isolate himself from his friends.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.
Maybe it's not a trap set by enemies, but rather an old self - defense mechanism of a long - lost village. The cave might be set to protect something precious within, and Naruto's presence accidentally triggered the defenses.
One possible fanfiction could be about Kushina finding Naruto in a situation where he's lost in a forest. Maybe she uses her unique chakra sensing abilities to track him down. It could be a heartwarming story of a mother reuniting with her son.
One possible scenario in this fanfiction could be that Naruto discovers an ancient and mysterious shrine in the forest. The shrine might hold some sort of power or secret. Maybe it has a connection to the Sage of Six Paths. Naruto, being his curious self, would likely start to explore it. He might find strange markings or artifacts inside that he has never seen before.
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.