One way to conceptualize a love story between Naruto and Pain could be through the idea of redemption. Naruto might see the pain and confusion in Pain's heart that led him to his extreme actions. He could strive to show Pain a different path, and in this process, a deep connection could form that might turn into love. Naruto's unwavering belief in the goodness of people could gradually break down Pain's walls.
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 For example, he could become withdrawn and isolate himself from his friends.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.
The biggest obstacle would be their conflicting ideologies. Naruto believes in the power of friendship and forgiveness to bring peace, while Pain believes in using force and instilling fear. It would be very difficult for them to overcome this fundamental difference in their worldviews and come together in love.
It happens after a significant amount of time spent on character development and side plots. Naruto returns when the story arc demands his presence for the next major conflict.
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.