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.
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.
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.
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.
Another theme is the power couple dynamic. Pepper is a strong and intelligent businesswoman, and Tony is a genius inventor. Their combined skills and how they support each other in both their personal and professional lives are often explored. For example, in some fanfictions, they work together to save Stark Industries from a major crisis. They use their unique abilities and the strength of their relationship to overcome difficulties.
Love and commitment are common themes. Since their relationship is central, many fanfictions explore how deeply they love each other and their commitment to make it work.
One common theme is redemption. After the events of Civil War, Tony often has to deal with the consequences of his actions, and many fanfictions explore his journey towards redemption, either within his team or in the eyes of the public. Another theme is rebuilding. His team might be fractured, so stories often revolve around rebuilding relationships and trust.
One common theme is the anticipation of parenthood. Tony might be shown as both excited and nervous about becoming a father. He could be constantly thinking about how to keep Pepper and the baby safe, especially considering his dangerous lifestyle as Iron Man.
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.