The fanfiction might explore how the child copes with this situation too. Is the child aware of the reasons? Does the child try to reunite the parents? There are so many possible storylines that can branch out from this one simple premise of Pepper leaving Tony with a child.
The story could also take a more dramatic turn. The child might develop some sort of special powers or abilities due to Tony's genes or the unique circumstances. This could attract the attention of new villains or other powerful entities, forcing Tony to not only protect his child but also the world from any potential threats that come as a result of the child's newfound powers.
At first, Tony might be in denial. He's so used to having Pepper by his side that he can't fathom her leaving, especially when she's pregnant. As time goes on, he could become very sad and start to reflect on what he did wrong in their relationship. He might try to win her back, using his resources and intelligence to show her that he can be a good partner and father.
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'.
Obviously, the main characters are Tony and Pepper. Tony is a complex character, a genius inventor and superhero. Pepper is his love interest and also a very capable businesswoman who often has to deal with the consequences of Tony's actions.
Well, perhaps Pepper realizes she and Tony have grown apart in some way. Maybe she feels neglected due to Tony's constant focus on his work or superhero duties. As for being pregnant, it could be that she discovers she's pregnant just as she decides to leave, adding a whole new layer of complexity to the situation. She might leave to protect the baby from the dangerous world that surrounds Tony.
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 Tony might become more withdrawn and less focused on the team, which could affect their mission planning.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.
Family is a very common theme. It often shows how Tony and Pepper build a family together and the joys and struggles that come with it. For example, they might deal with the child's first steps in the scientific world if they inherit Tony's talent.
In the fanfiction, Pepper could find out she's pregnant right before a major crisis that Tony has to deal with. She has to be strong on her own while he's away, and when he comes back, he realizes how much she has sacrificed. This leads to a deeper bond between them and a stronger determination to create a happy family.
One popular Tony and Pepper child fanfiction is 'The Stark Family Legacy'. It beautifully portrays their life as parents and the challenges they face raising their child. It shows how Tony's genius and Pepper's strong will combine to shape their family's future.