They could have a mentor - mentee relationship. Pepper, being experienced in many aspects of life, can guide the daughter. She can teach her about leadership and responsibility, just as Tony has taught Pepper over the years. This way, the daughter can grow up to be a strong and capable woman.
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.
It could be some business rivals who see the daughter as a threat to their plans. They might try to undermine her or use her to get to Stark Industries.
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.
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.
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.
The relationship could develop gradually. Peter would show his gratitude towards Tony and Pepper for taking him in. Tony would see Peter as not just a protege but also as a son. He would share his knowledge and experiences with Peter. Pepper would be involved in Peter's daily life, making sure he has everything he needs. For instance, she might cook his favorite meals or help him with his schoolwork. As they go through various challenges together, their bond would strengthen.
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.
A common theme could be family legacy. Since she's Tony Stark's daughter, there would be the pressure and pride of carrying on his name. Another theme might be self - discovery. She has to figure out who she is outside of being a Stark. For example, she might discover a passion for art or music that has nothing to do with her father's technological world.
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.
Perhaps the story is set in a future where new threats emerge. The daughter, with her combined Stark and Potts genes, becomes a key figure in defending the world. She teams up with other young superheroes and uses her intelligence and courage to overcome the villains. It could also involve her uncovering some long - lost secrets of her father's that help in the fight.