One possible plot twist could be that Tony is actually working on a top - secret project that he has to keep from Pepper for her own safety. The Avengers misinterpret his secretive behavior as cheating. For example, he might be collaborating with a female scientist who has some unique skills relevant to the project. The Avengers see them together often and jump to conclusions.
I think Natasha would be the first to discover the truth. She's very perceptive and good at reading people. If she noticed something strange about Tony's behavior, she would start investigating. She has the skills to follow him secretly and figure out if he's really cheating or if there's something else going on. Maybe she'd find out that he's just trying to surprise Pepper with a big anniversary gift and all the secrecy is part of the plan.
Maybe in the fanfiction, Pepper leaves Tony after a big argument about his recklessness. He's always putting himself in danger, and she can't take it anymore. She leaves to find herself and pursue her own career goals that she had put on hold for him. Tony then has to learn to be more responsible and make some changes in his life if he wants her back.
Maybe in the fanfiction, Tony leaves Pepper due to his own self - doubts. He might think that he is not good enough for her, perhaps because of his playboy past or his superhero lifestyle which often brings chaos and destruction. So he chooses to leave to spare her from his 'imperfections'.
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.
One possible plot twist could be that as a girl, Tony Dinozzo uses her charm and different perspective to solve cases in a unique way. For example, she might be able to get closer to female suspects or witnesses who would be more open to sharing information with another woman. This could lead to faster case resolutions and a different dynamic within the team.
One possible reason could be jealousy. Maybe Tony's intelligence and wealth made some Avengers feel inferior, and over time, that festered into betrayal. For example, if Tony developed a new technology that could potentially overshadow their own abilities, they might feel threatened.
In some fanfictions, there could be a plot twist where Pepper is kidnapped not by the main villains of Iron Man 3 but by a secret organization that has a vendetta against Tony. This forces Tony to not only fight his known enemies but also this new threat, all while trying to rescue Pepper. It would make for an exciting and different take on their story in the context of Iron Man 3.
Perhaps Pepper Potts would interact with each Avenger in unique ways. For example, she could have in - depth conversations with Tony Stark about how his superhero activities affect their business. With Captain America, she might discuss the values and ethics of the Avengers' actions. And with Thor, she could be fascinated by the Asgardian culture he represents.
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.
One possible plot twist could be that Bucky and Steve initially protect Tony out of duty, but then they discover a deeper connection between them all. Maybe they find out that Tony has been unknowingly targeted by a common enemy from their past. Another plot twist could be that while protecting Tony, they accidentally expose a secret of Tony's that he was trying to keep hidden, which then leads to a whole new set of challenges for all of them. It could also be that the way they protect Tony causes a rift in the superhero community, as some might think they are being too overprotective or that Tony doesn't deserve such protection.