Perhaps in the fanfiction, he fails to protect the world from a new and powerful threat. Tony always sees himself as a protector. If his inventions or plans don't work and many lives are lost, he would feel an overwhelming sense of guilt and that could lead to him crying.
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.
It could be related to his relationship with Pepper. If Pepper were in danger or they had a big fight and she decided to leave him. Pepper has been a very important part of his life. Her absence or the thought of losing her would surely make Tony emotional enough to cry.
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 reason could be that he's frustrated with the leadership or the direction the Avengers are taking in the fanfiction. He might feel his ideas are not being heard.
Perhaps he leaves for personal growth. America has become a place full of painful memories for him, like the loss of friends during battles that happened on American soil. So, he decides to start anew in another place.
Maybe his own self - centered nature plays a role. Tony Stark has always been a bit of a playboy and a genius focused on his own projects. His daughter might seem like an afterthought compared to his latest invention or business deal.
Maybe he doesn't fully understand his powers yet. Tony Stark is a scientific genius, but new powers might be beyond his current understanding. He could be worried that if he reveals them too soon, he won't be able to control them properly and might cause harm. So, he chooses to hide them while he studies and figures them out.
One interesting fanfiction could be where Tony Stark cries after realizing the true cost of his superhero lifestyle on his personal relationships. He might break down when he sees how his actions have pushed away Pepper or Rhodey.
Tony Stark may dislike Avengers fanfiction because it can mess with the emotional core of the team. The real relationships between the Avengers are deep and complex. Fanfiction might simplify or distort these relationships. For instance, his friendship with Steve Rogers has many layers, and fanfiction could make it into something that doesn't do justice to their real bond. Also, he's a man who values his privacy to an extent. Fanfiction might delve into his personal life in ways that he doesn't appreciate, making him feel exposed and misrepresented.
One possible reason could be a major disagreement. Maybe the Avengers made a decision that Tony strongly opposed, like a dangerous mission plan that he thought was too risky. For example, if they decided to team up with a morally ambiguous character without proper precautions. Another reason might be personal issues. Tony could be going through something in his personal life that makes him want to distance himself from the group, like dealing with the stress of his identity as Iron Man being public and feeling the Avengers draw too much unwanted attention.
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.