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 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 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.
One possible reason could be a disagreement over superhero tactics. Peter, being young and idealistic, might yell at Tony if he thought Tony's methods were too extreme or not in line with his own sense of justice. For example, if Tony made a decision during a battle that put civilians at risk, Peter would likely be very vocal about it.
One reason could be the loss of a close friend like Steve Rogers. Their complex relationship and the times they fought side by side, if Steve were to sacrifice himself, it would be a huge blow to Tony. He might cry out of grief and also regret for the times they had disagreements.
The fanfiction could start with their individual backstories that led to this trouble crying. Tony's past with his parents and his journey as a superhero has made him suppress his emotions. Peter, growing up without a father figure for a long time, has learned to be tough. As they work together more often, small incidents start to crack their emotional walls. For example, a kind word from a civilian they saved makes Peter's eyes water a bit, but he quickly holds it back. Tony notices and it makes him reflect on his own emotional state.
The theme of legacy is often present too. Peter might be crying while thinking about how to carry on Tony's legacy. He may feel the weight of living up to Tony's name and the expectations that come with it. Fanfictions may delve into Peter's internal struggle as he tries to figure out how to be the hero Tony believed he could be, all while dealing with his own emotions.
Well, it could be that in the fanfiction, baby Peter shows some extraordinary abilities even at a very young age. Tony Stark, being the genius he is, wants to study Peter to figure out how his powers work. But at the same time, he also becomes very protective of Peter like a father figure. They might have some cute moments where Peter tries to imitate Tony's high - tech gadgets with his baby toys.
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.
One possible fanfiction could be where they are in a battle against a powerful new villain. Peter Parker might get hurt while trying to protect civilians, and Tony Stark, in his attempt to save Peter, also gets injured. This could lead to a heart - wrenching scene where they both have to rely on each other's strength to get through the situation and back to safety.
A fanfiction might involve Peter Parker and Tony Stark being kidnapped during a mission. They are held in a high - security facility. While kidnapped, Tony uses his wits to analyze the security system, and Peter uses his enhanced senses to gather information about their captors. Eventually, they manage to outsmart their captors and escape.