Perhaps the fanfiction could explore the challenges they face due to their different natures. Elijah being a vampire and Bonnie being a witch. There could be concerns about the health of the baby, with Bonnie using her magic to ensure a safe pregnancy and Elijah struggling with his vampiric instincts, like the urge to drink blood while being around his pregnant partner.
Maybe the pregnancy was unexpected and it forces Bonnie and Elijah to re - evaluate their relationship. They might have been in a somewhat tenuous relationship before, and now they have to come together for the sake of the baby. There could be a journey of them learning to trust each other more deeply, dealing with family reactions (Bonnie's witch friends and Elijah's vampire family), and ultimately finding a way to build a future for their new family.
You can start by looking on fanfiction websites like Archive of Our Own (AO3) or FanFiction.net. These platforms have a large collection of fanfictions on various topics, including ones about Bonnie and Elijah. Just use the search bar and type in 'Bonnie and Elijah pregnant' and you'll likely find some relevant stories.
A possible plot could be that Bella and Elijah are from different species in the fanfiction world, for example, one is a vampire and the other a werewolf (assuming such a scenario exists in this fanfic). Their pregnancy is then a very unique situation that defies the norms of their world. This could lead to a lot of drama, with different factions either trying to protect or harm them because of the baby. They would have to rely on each other and a few trusted friends to navigate this new and dangerous situation.
One idea could be that Elijah discovers he is going to be a father during a time of great turmoil in the supernatural world. His family's enemies might see this as a weakness and target him and his unborn child. Another plot could involve Elijah trying to protect the mother of his child from the dangerous vampire politics and ancient curses that could harm her or the baby. Maybe he has to make a deal with a powerful witch to ensure a safe pregnancy for the mother.
One idea could be that Bonnie discovers she's pregnant during a time of great chaos in the magical world. She has to keep it a secret while trying to protect herself and her unborn child from dark forces. Another could be a story where the father of the baby is a mystery, and Bonnie goes on a journey to figure it out all while dealing with the physical and emotional changes of pregnancy.
One idea could be that Bonnie discovers she's pregnant during a time of great turmoil in the supernatural world. She and Stefan then have to figure out how to protect their unborn child from all the threats. Maybe they go into hiding, and along the way, they face challenges that test their relationship and their will to survive.
One idea could be exploring how the other characters in the FNAF universe react to Bonnie's pregnancy. They might be confused, excited, or worried. Another could be the challenges Bonnie faces during the pregnancy, like dealing with her animatronic body limitations.
Damon would likely make sarcastic remarks at first but deep down be happy for them. He and Bonnie have a long history, and he'd come around to being supportive. Elena would be very emotional. She'd be there for Bonnie, offering advice based on her own experiences, even if they were different in nature. The other witches in Bonnie's coven might be a bit worried at first, fearing that the pregnancy could disrupt Bonnie's connection to magic or put her in danger from other supernatural forces.
One idea could be that they face challenges from the supernatural community due to their unborn child's potential power. The other vampires or witches might see the baby as a threat or a valuable asset. Another plot could be them preparing for the arrival in a world full of danger, like building a safe haven and gathering allies.
One plot idea could be the challenges they face in keeping the pregnancy a secret from their enemies. Another could be how they prepare for the arrival of the baby in a world filled with supernatural threats. For example, they might have to find a safe place away from the constant power struggles in their supernatural community.