One possible plot could be that Dark Tony has some sort of vendetta against Peter. Maybe he believes Peter has something that belongs to him, like a piece of technology or some secret information. So, he kidnaps Peter to get it back. He might hold Peter in a secret lair and try to force the information out of him. This could lead to a series of events where Peter tries to escape and outwit Dark Tony.
Another possibility is that Doctor Strange could rescue Peter. He has powerful magic and the ability to travel through different dimensions. He might sense that Peter is in danger through his magic and use his powers to find Dark Tony's lair and free Peter. Strange could also use his magic to fight off Dark Tony if he tries to stop the rescue.
In the 'tony hits peter fanfic', it could be set in a situation where an external force is influencing Tony's actions. Maybe an enemy has some kind of mind - control device on Tony. So, Tony hits Peter without his true self being in control. Peter then has to figure out what's wrong with Tony and find a way to break the mind - control, all while dealing with the physical and emotional pain of being hit by someone he looks up to.
One possibility is that Wade has some sort of misunderstanding. Maybe he thinks Peter is in danger from some other villains and kidnaps him to keep him safe. He might take Peter to a secret hideout where Peter initially struggles but then realizes Wade's intentions are not entirely malicious.
One possible plot twist could be that Loki actually has a noble reason for kidnapping Tony. Maybe he wants to use Tony's intelligence to stop a greater threat that the other Avengers are unaware of. For example, there could be a hidden enemy that Loki has knowledge about, and he believes only Tony can help create a device or strategy to defeat it.
One possible plot could be that the Winter Soldier is under some mind control still and is made to believe Tony is a threat to a certain organization. So, he kidnaps Tony to bring him to his handlers. But during the journey, some of the Winter Soldier's old memories start to surface, which makes him question his mission.
It could also be for revenge. Perhaps Stiles or someone associated with him has wronged Peter in the past within the context of the fanfiction story. So, Peter kidnaps Stiles to get back at him or those related to him. Another reason might be that Peter is being controlled by some other force. There could be a dark entity manipulating Peter's actions, and it makes him kidnap Stiles for its own sinister purposes.
In a fanfiction sense, Tony might kidnap Peter due to a misunderstanding. For example, if Peter was involved in some sort of experiment that Tony misinterprets as dangerous. He could be worried that Peter is being influenced by the wrong people or powers, so he kidnaps him to figure out what's really going on. Tony's actions, although extreme, could be driven by his love and concern for Peter as a mentor.
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.