The main antagonist could be a character within their own group who has turned bad. This person might be jealous of the relationship between Steve, Tony and Peter. They spread rumors and lies, which ultimately leads to Steve believing that he is not welcome or that he is causing more harm than good, and so he leaves.
Maybe it's an old enemy of Steve's who wants to isolate him. By driving a wedge between Steve and his friends Tony and Peter, the antagonist can make Steve more vulnerable. This enemy could use false information to make Tony and Peter distrust Steve, which in turn makes Steve think it's best for him to leave.
It could be a new villain who has the ability to manipulate minds. This villain could make Steve believe that he is a danger to Tony and Peter, causing him to leave. For instance, the villain might implant false memories or thoughts in Steve's head, making him think that his actions might accidentally harm them in the future.
One possible main antagonist could be a villain who is jealous of Tony's resources and sees Peter as a way to get to him. Maybe someone like Justin Hammer, who could try to manipulate Peter into betraying Tony and Steve.
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.
It could be someone from Stark Industries who doesn't like the idea of Peter inheriting something. Maybe a rival within the company who sees Peter as an inexperienced kid and wants to take whatever Tony left for Peter for themselves.
It could be a scientist who is jealous of Tony's inventions. He creates a device that causes the hiccups as a way to disrupt Tony and Peter. His goal might be to steal Tony's technology while they are distracted by the hiccup problem.
It could also be that some of Thanos' followers or those who try to take advantage of the post - snap chaos become the main antagonists. For example, some of the rogue elements in the universe might see this as an opportunity to gain power and territory, and they would oppose the Avengers who are trying to restore order. So they could step up as the main threats in the fanfiction.
The main plotline could involve the boys' school life. Peter is a young superhero but also a student. Tony and Steve might have different ideas on how involved they should be in Peter's school. Maybe Tony wants to use his influence and technology to enhance Peter's education, while Steve thinks Peter should have a normal school experience. Also, the story could revolve around protecting Peter from villains who find out he is now under the protection of two of the most powerful Avengers. This could lead to some intense battles and the strengthening of their family bond through these trials.
Maybe it's an old clock - maker named Mr. Grimsby. He has a dark past related to a cursed clock he once made. When he hears about Tony's interest in clocks, he fears that Tony will discover his secret. So he tries to stop Tony from delving deeper into the world of clocks by causing problems in Tony's life, like getting him fired from his job at the local clock shop.
It could be Nancy's over - controlling mother. She might be against the pregnancy and try to force Nancy to make certain decisions, like giving the baby up for adoption against her will.
It could be a powerful underworld lord who doesn't want Naruto to leave. This lord might see Naruto as a threat to his rule in the underworld.
An ancient and powerful Pokémon with the ability to influence Pikachu's mind could be the antagonist. It might see Pikachu's potential and wants to use it for its own dark purposes. By making Pikachu leave Ash, it can start to manipulate Pikachu more easily.