Maybe Peter inherits Tony's high - tech gadgets. For example, he could get access to some of Tony's Iron Man tech, which would be a huge deal. This could set him on a new path in his superhero journey, perhaps allowing him to upgrade his own suit or develop new abilities.
In this fanfiction, it could be that Peter snaps after Tony makes a decision that Peter strongly disagrees with. Let's say Tony decides to sacrifice a certain group of people to save the majority in a moral dilemma. Peter, who has a stronger sense of justice for the individual, snaps and decides to go against Tony's plan. He then has to fight not only the external threat but also deal with the rift he has created within the team.
One possible plot could be that Peter has continuously disobeyed Tony's safety instructions while working in the lab or on some high - tech projects. Tony, out of frustration and a sense of responsibility, resorts to this rather extreme form of discipline. However, this kind of plot would be quite controversial and not in line with the general positive and heroic image of their relationship in the mainstream stories. It would also be a very different take on their characters, showing a more authoritarian side of Tony.
Perhaps Steve leaves because of a personal sacrifice. He might discover that his presence is putting Tony and Peter in danger, like there's a villain targeting those close to him. So, to keep them safe, he leaves without much explanation. It could also be that he has some unfinished business from his past that he has to attend to alone, which forces him to part ways with Tony and Peter.
The fanfiction could also focus on the emotional bond between them. Maybe Peter gets into a dangerous situation and Tony has to face his worst fears of losing his son. This could lead to a deeper understanding of their relationship and how they rely on each other not just as superhero partners but as father and son.
It could also be due to external pressure. The media or some powerful figures in the fanfiction world might force Tony to stay away from Peter. They could spread false rumors about their relationship or use their influence to separate them for their own gain.
Well, perhaps in the fanfiction, Tony kidnaps Peter because he believes Peter has some sort of secret that could endanger the world if it gets out. He might be trying to protect the world in his own, extreme way. And Peter is left confused and scared, having to figure out how to convince Tony he's on the right side.
Well, perhaps Tony has some sort of misunderstanding. Maybe he thinks Peter has betrayed him in some way, so he kidnaps Peter. But later, as he realizes his mistake, he tries to make it up to Peter.
Well, one possibility is that Tony could replace Peter in a mission. Maybe Peter gets injured and Tony steps in to finish what Peter started. It could also be about Tony taking over Peter's role in a social or school setting within the fanfiction world.
In the fanfiction world, there could be a prophecy or a pre - determined fate that Tony believes in. He may think that Peter's sacrifice is necessary to fulfill this prophecy and save the world from some greater threat related to the Soyl Stone. He might see it as a selfless act in the long run, even though it seems cruel.
One possible plot could be Peter growing up in the Stark mansion, having access to all of Tony's technology. He might start inventing things at a very young age. And when he gets his spider - powers, Tony could be more directly involved in helping him develop his suit and his skills as a superhero.