It could be that after a big battle, Tony is presumed dead. But then he shows up alive, much to Pepper's surprise and joy. She is over the moon. They talk about how they've changed during the time apart and reaffirm their love for each other. Tony might even promise to be more careful in the future for her sake.
Maybe Tony has been lost in space or some other difficult situation. When he finally makes his way back, Pepper is waiting at the Avengers compound. Their reunion is filled with emotions. Pepper might be a bit angry at first for him putting himself in danger, but then she realizes how much she missed him and they share a passionate kiss.
Their relationship could become stronger. After being apart and facing the possibility of losing each other, they might cherish each other more. They could start to be more open with their feelings and communicate better.
One possible scenario could be that they meet in a familiar place, like the old NCIS office. They might exchange some witty banter at first, just like in the old days. Then, they could start reminiscing about their past cases together.
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.
Overcoming challenges together is also a big theme. Whether it's dealing with a new supervillain threat or internal issues within the Avengers, Tony and Pepper often face difficulties side by side. Fanfictions explore how their love helps them get through these tough times, and how they grow both as individuals and as a couple.
If Pepper leaves Tony in the fanfiction, it could disrupt the Avengers' dynamic. Tony might become more withdrawn and less focused on the team, which could affect their mission planning. For example, he might not be as quick to come up with technological solutions during battles.
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.
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.
There's a fanfiction called 'Pepper's Perspective'. This one gives a detailed view from Pepper's point of view. It delves into how she manages her relationship with Tony while being in the middle of all the superhero chaos. It's quite interesting as it shows her strength and her love for Tony in a new light. She has to deal with Tony's risky superhero stunts and also keep Stark Industries running smoothly.
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.
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.