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.
One possible storyline could be that the Avengers are under some form of mind control. Maybe a powerful villain has manipulated them into believing Tony is a threat to the world. So, they start to target him, causing both physical and emotional harm. For example, they might break into his workshop and destroy his latest inventions, which are not only his creations but also his passion.
A possible storyline could be a technology exchange. Tony is always eager to get his hands on new tech, and Wakandan technology is extremely advanced. So, he could visit Wakanda to learn about vibranium and its applications. T'Challa, in turn, might be interested in Stark Industries' clean energy solutions. This could lead to a series of events where they work together to improve both their technologies and in the process, form a strong friendship.
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.
In some fanfictions, their relationship deepens as they face new challenges together. The events of the Avengers might have made them realize how much they need each other. So they become more supportive and understanding of one another. For example, Tony might be more open with Pepper about his fears and insecurities.
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.
Maybe in the fanfic, Tony uses time travel technology to go back in time to a moment before he met Pepper Potts. He then tries to avoid getting involved with her for some noble but misguided reason. However, his future daughter, who has knowledge of the 'right' timeline, comes back in time to set things straight and make sure her parents get together. She could be like a guardian of their relationship and the timeline related to it.
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.
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.
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.
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.