The theme of sacrifice is also quite prominent. Tony might have to sacrifice some of his ideals or relationships for the greater good in the Civil War context, and Pepper might have to sacrifice her own wants and needs to support Tony. Also, the theme of trust is there. They need to trust each other even when things are falling apart around them in the war.
A popular Tony and Pepper Civil War fanfiction is 'Together Through It All'. In this one, the author does a wonderful job of depicting how their relationship evolves. It shows Pepper being a strong presence in Tony's life as he navigates the complex situations in the Civil War. There are parts where they face difficulties together and it really shows the strength of their bond.
One scenario could be that during the events of the Civil War, Pepper discovers a way to secretly support Tony without getting directly involved in the conflict. She uses her business acumen to manipulate some of the political and economic aspects that are affecting the situation. For example, she could be working behind the scenes to secure resources for Team Iron Man, like getting better deals on equipment or finding legal loopholes to keep their actions within the law.
Often, their relationship is tested. Tony's involvement in the Civil War can cause stress between them. Pepper might worry about his safety and the moral implications of his actions.
One idea could be that Pepper tries to mediate between Tony and Steve during the Civil War. Since she knows Tony so well, she might be able to find common ground that others can't. Another could be Pepper getting involved in the fight herself, using her business acumen and strategic thinking to help Tony's side. Maybe she discovers a hidden plot that could change the course of the war.
One way a fanfiction could explore their relationship is by having Pepper be directly involved in some of the events of the Civil War on Tony's side. This would put a strain on their relationship as they are both in the middle of danger. They would have to rely on each other more than ever, and this could bring out new aspects of their love. For example, Tony might realize how much he needs Pepper not just as his partner but also as a strong ally, and Pepper could see a more vulnerable side of Tony that she hadn't seen before during the battles and political maneuverings of the Civil War.
In some Civil War fanfictions, Tony might die due to a malfunction in his suit during a battle. Maybe an enemy manages to hack into it and cause a critical system failure that leads to an explosion.
In this fanfiction, Pepper might struggle a bit with the idea of being pregnant while Tony is constantly in the spotlight as Iron Man. She could worry about how their child will grow up in such a public environment. However, Tony reassures her that they can create a normal family life within their extraordinary circumstances.
In the fanfiction, Pepper being pregnant could be a factor that tries to pull Tony out of the conflict. It could make him question the point of the war when he has a family to think about. Maybe it causes him to try and find a more peaceful solution, or at least stay on the sidelines more.
Conflict of ideals is also a major theme. Natasha and Tony have different views on things like superhero registration. In fanfictions, this often leads to intense arguments and moments of self - reflection as they both try to justify their stances and understand the other's point of view.