Perhaps in the fanfic's storyline, Tony is facing a lot of pressure himself, like threats from powerful villains or issues within the Avengers. Peter's actions, whether they are mistakes or just inconvenient timing, could be the straw that breaks the camel's back for Tony, causing him to yell at Peter.
Peter might be initially shocked and a bit scared. After all, Tony is like a mentor to him. But then he could become defensive, trying to explain his actions or point of view.
Perhaps Peter failed to follow Tony's instructions regarding some important technology or protocol. Tony, being a perfectionist and concerned about safety, would then yell at Peter for not listening. In the fanfiction world, this kind of conflict adds drama and tension to their relationship.
Maybe Peter misses an important training session. Tony has probably put a lot of effort into training Peter to be a better superhero. If Peter skips out on training for something unimportant, like going to a party or just being lazy, Tony would be justifiably angry and yell at him for not taking his superhero responsibilities seriously.
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.
On the other hand, it could also be a turning point for the better. Sometimes a big outburst like that can clear the air. They might realize they've been misunderstanding each other and start to work on their relationship more effectively after the initial shock of the yelling.
Well, perhaps Peter is frustrated with the Avengers for not including him in a crucial mission. Maybe he feels overlooked and underestimated, so he yells at them to voice his anger and disappointment.
The main antagonist could be the Avengers' own bureaucracy or leadership structure. Peter might be yelling at them because their rules and decision - making processes are preventing them from doing the right thing. He might see this as a hindrance to their ability to protect the world effectively and is frustrated enough to yell at them to try and bring about change.
Peter could stand up to Tony. By showing his strength and not taking Tony's meanness lying down, he might earn Tony's respect. For instance, if Tony makes a snide comment, Peter could give a smart comeback that makes Tony see him in a new light.
One aspect to consider in 'possessive Tony and Peter fanfiction' is the nature of their relationship. It might explore themes of protection. Tony could be possessive in a way that he wants to keep Peter safe from the various dangers in the Marvel universe, like powerful villains.