In some cases, the writer might be trying to make a statement about the nature of relationships in general. They could be using the Pepper - Tony relationship as an example to show how even seemingly perfect relationships can have cracks. Or perhaps they are simply exploring a 'what if' scenario out of pure creativity, without any deep - seated motives other than to see where the story could go from such a shocking start.
Maybe the writer wants to explore an alternate view of Pepper's character. They could be showing that she has flaws and isn't the perfect partner all the time. It could also be a way to introduce new characters into the story in a more impactful way, like the person she cheats with.
It could be that Tony is under some sort of mind - control or influence that makes him cheat on Pepper. Then the story might focus on Pepper's journey to break the control over Tony and save their relationship.
I'm not sure if there is truly 'good' fanfiction in this regard as it goes against the general positive relationship depicted in the main story. Fanfiction often contains a wide range of interpretations, but this particular theme might not be in line with what most fans expect from the Pepper - Tony relationship.
On the other hand, some fans might be interested in seeing how the author develops the story from such a controversial starting point. They could be curious about how Pepper will respond and if there's a chance for redemption for Tony.
Power hunger could be a motive. Tony already has a lot of power with his technology, but if he becomes obsessed with having more and more, it could lead him to evil. He might start to see others as obstacles to his power gain.
Perhaps Pepper, in an attempt to protect Tony from himself, takes extreme measures. For example, she could sell off Stark Industries' technology that Tony was using for his Iron Man suits without his consent. This would be a huge betrayal in Tony's eyes as his technology and the Iron Man identity are so closely tied to him. It could lead to a rift between them that is difficult to mend as Tony feels violated and Pepper believes she was doing the right thing to keep him safe.
One possible motive could be a misunderstanding. Maybe Steve believes Tony has done something that endangers the team or the world, but he's misinformed. Another could be that Steve has been mind - controlled. In some fanfictions, external forces take over Steve's mind and make him do things he wouldn't normally do, like kidnapping Tony.
One possible plot could be that Tony, due to some external pressure or misunderstanding, gets involved with another character while in a relationship with Loki. Maybe he's forced into a political alliance that looks like cheating to Loki. Another could be that Tony's self - destructive tendencies lead him to make a mistake and cheat, causing a rift in their relationship that they then have to struggle to repair.
One possible motive could be to create drama. Writers might think that by introducing such a controversial plot, they can attract more readers who are interested in seeing how the story would unfold in this unexpected direction.
One possible plotline could be the daughter inheriting Tony's genius and getting involved in some high - tech project at a young age. For example, she might build her own mini - Iron Man suit.
Another storyline could be that they get involved in training the next generation of superheroes or tech - savvy individuals. They realize the importance of passing on their knowledge and skills. Tony could teach about advanced engineering and Pepper could offer her business and leadership expertise. This would be their way of ensuring a better future for the world.