Clara being pregnant in a Doctor Who fanfiction could cause a shift in the dynamic of their relationship. Maybe it forces them to confront their feelings more deeply or makes them reevaluate their priorities. It could even inspire a quest to find a safe haven for Clara and the baby in the midst of the chaos of time and space.
Well, it could lead to all sorts of adventures and challenges for the Doctor and Clara. Maybe they have to protect the unborn baby from some cosmic threat.