It's popular because it shows his vulnerability. Peter Parker is often seen as a strong hero, but when he cries in fanfiction, it humanizes him more. Fans like to see this different side of him.
One possible scenario in such a fanfiction could be that Peter is crying because he misses Tony Stark after his death. Tony was like a mentor to Peter, and his absence leaves a huge void. Peter might be in the Avengers compound, looking at old photos or mementos of Tony, and the memories make him break down in tears.
One common theme is loss. Whether it's the loss of a loved one like Uncle Ben or a close friend, it often leads to Peter breaking down in tears. It's a way to explore his human side and how he deals with grief.
One popular theme is loss. Peter could be mourning the death of someone close to him, like Aunt May or a fellow superhero. This makes him break down and cry as he tries to cope with the emptiness. Another theme is self - doubt. He might question his abilities as Spider - Man, which leads to him crying in despair. For example, if he fails to save a civilian, he starts to think he's not worthy of the mantle. Also, unrequited love is a common theme. Peter might have feelings for someone who doesn't feel the same way, and this causes him to cry in private.
One good example could be a fanfiction where Peter Parker cries after losing a dear friend in a battle. The author might describe his trembling lips and the silent sobs that rack his body, really delving into his emotional turmoil.
One popular 'Peter Parker crying fanfic' could be 'The Weeping Spider' which delves deep into Peter's emotional turmoil after a major loss in his life. It shows his vulnerability and how he copes with the pain.
One great 'Crying Peter Parker' fanfiction could be about him mourning the loss of a dear friend like Ned. In the story, Peter might be sitting alone in his room, looking at old photos and just breaking down. He'd remember all the good times they had, from building Lego Death Stars to sharing secrets. Another could be Peter crying because he feels he's failing as Spider - Man, constantly getting beaten down by villains and not being able to protect the city as he should. He might be on a rooftop, tears streaming down his face as he contemplates giving up. And then there's the possibility of a story where Peter cries because he's in love but can't have the relationship due to his dangerous life as Spider - Man. He watches the person he loves from afar, with a single tear rolling down his cheek.
One possible scenario in a fanfiction could be that Peter Parker is trying to hide his emotions from Tony Stark. Maybe he's been through a tough situation at school, like being bullied, but he doesn't want to seem weak in front of his mentor. Tony, on the other hand, has his own issues with showing vulnerability. He's always been the strong, confident Iron Man. But perhaps he starts to notice Peter's struggle and tries to open up about his own past traumas to encourage Peter to let it all out.
A reason could be that Peter is reminded of Tony's last words to him. Those words were full of hope and trust in Peter. When Peter reflects on them, he is overcome with emotion and starts to cry as he feels the weight of Tony's expectations.
One popular fanfiction site is Archive of Our Own (AO3). You can go there and search for 'Peter Parker crying over Tony Stark' to find relevant stories. There are likely many works that explore the emotional bond between them and scenarios where Peter might be crying over Tony's death or other significant events in their relationship.