Perhaps there have been some recent events in the fanfic that made Castle feel more vulnerable about their relationship. For example, Beckett might have received a job offer in a far - away place, or there could have been a misunderstanding that made Castle think she was pulling away from him. This would make him terrified of losing her as she has become an integral part of his life.
It could be that he realizes how much Beckett means to him on a deeper level. She's not just a colleague but someone he truly cares about. He might be terrified because he envisions a future without her by his side, especially considering the dangerous cases they often deal with where something could happen to her at any time.
Maybe he's afraid of losing her because she's his partner and they've been through so much together. Their relationship is very important to him.
He might become more protective. He'll be constantly on guard to make sure nothing bad happens to Beckett.
One possible reason could be that they are on a secret mission. Maybe they are trying to protect a key witness or important evidence from a powerful and dangerous criminal organization. In the world of fanfic, this could lead to them having to disappear to keep their whereabouts unknown.
Maybe they stumble upon a government conspiracy. The government wants to keep something hidden and they are seen as a threat, so they are made to disappear. It could also be related to a scientific experiment gone wrong. They are in the wrong place at the wrong time and get caught in an energy field that transports them to an unknown location, causing them to disappear from their normal world.
Perhaps they are trying to protect their relationship from outside interference. For example, if there are people in Castle's publishing world or Beckett's police department who don't approve of their relationship, they could pretend to be separated to avoid any negative consequences. This would allow them to still be together in private while keeping up the appearance of being single in public. Also, it could be a way to test their relationship. They might want to see how they would fare on their own and if their feelings for each other are strong enough to withstand a period of 'separation'.
Maybe he saw Beckett spending a lot of time with another man without knowing it was for a case. Castle is a bit of a jealous type, and he might overreact to normal interactions.
It could be that Castle is overprotective. He loves Alexis so much that even the slightest sign of Beckett not being on the same page as Alexis in Castle's eyes makes him think Beckett hurt her. Maybe Beckett gave Alexis some career advice that Castle thought was too pushy.
A Castle and Beckett baby fanfic could be about their journey into parenthood. It might explore how they adjust to having a baby in their lives. For example, Castle could be super excited and start writing new stories inspired by his new family experience, while Beckett might be a bit more cautious and protective.
Jealousy could also play a part. Castle is often surrounded by beautiful and adoring fans as a famous writer. Beckett might start to feel insecure, especially if she sees some of these fans getting a bit too close to Castle. On the flip side, Beckett's dedication to her work and her male partners in the police force could make Castle jealous, ultimately leading to their break - up.
One possible plotline could be that the baby has some sort of special ability or is in some way connected to a mystery they have to solve. Maybe the baby's birth coincides with a strange series of events in the city, and Castle and Beckett have to use their skills to protect the baby and figure out what's going on.
In a fanfic where they have a baby, their relationship would shift. They would now be partners not only in crime - solving but also in parenting. Castle would likely become more domesticated, helping with diaper changes and midnight feedings. Beckett would have to learn to let Castle in more on the parenting front, and they would communicate more about family - related matters. This new aspect of their relationship would add a different layer of complexity and closeness to their bond.