Well, it could be that Tony is focused on protecting Morgan and sees Peter as capable of handling himself, which leads to him ignoring Peter. And Peter might get hurt in a dangerous situation that he wasn't fully prepared for.
It's possible that Tony's priorities shift towards Morgan, thinking Peter is resilient. Peter could get hurt when he takes on a challenge alone without Tony's support and underestimates the danger.
Maybe Tony has to focus more on Morgan's needs at that moment and doesn't have enough time for Peter.
Maybe Tony has a special interest in Harley in the fanfiction. His focus is completely drawn to Harley, so he ends up ignoring Peter. It could be that Harley has some unique qualities or abilities that Tony finds more appealing at the moment.
Well, in some fanfictions, Morgan might hate Peter because she could be jealous of the attention he gets from the other Avengers or people around them. Maybe she feels that Peter is taking away the spotlight from her or her family in some way.
In many Disney Peter Pan fanfictions, Peter Pan does get hurt. Writers may do this to add depth to his character. When he gets hurt, it can lead to different reactions from the other characters in the story, like Wendy taking care of him. It also allows for a different kind of growth in the story. For example, he might become more cautious or learn a valuable lesson about his overconfidence. And it can also create new storylines where the characters have to find a way to heal him, which can be very interesting to read.
One reason could be pride. Tony might see Peter as a sort of protégé, and just like a teacher or mentor is proud of their student's achievements, he brags. He's invested time and energy into Peter, and when Peter does well, it reflects well on Tony too.
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.
At first, it's a bit rocky. Peter is used to being on his own, and Tony has his own way of doing things. But as they spend more time together, they find common ground. Tony helps Peter with his schoolwork, especially in science - related subjects. Peter, in turn, shows Tony the importance of having a pure heart in the superhero world. They go through challenges together, like fighting villains side by side, which deepens their bond.
It could be that Tony is there to check out the school's science facilities. He might be interested in funding some new projects or upgrading the existing ones. Since Peter is his protege, he wants to make sure that the school provides a good environment for Peter to grow his scientific knowledge. Also, he may be scouting for new talent among the students. He knows that young minds can come up with fresh and innovative ideas, and Peter's school could be a great place to find the next generation of inventors and scientists.
Another reason could be related to Peter's mistakes. He may make errors during a mission that put the whole team or the city at risk. Tony, who has a lot of responsibility on his shoulders, might yell at Peter as a way to make him understand the seriousness of his actions and to prevent future mistakes.
Often in fanfiction, Ego's actions towards Peter Quill are harmful. His grand plans might involve sacrificing Peter in some way. He could have lured Peter to his planet with false promises of a family and a great destiny, only to reveal that Peter was just a tool for Ego to consume more planets and gain more power.