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 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.
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.
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.
Maybe in the fanfic, Beckett got a new job opportunity in a far - away place. This could make Castle think she's leaving him.
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'.
One possible reason could be differences in their long - term goals. Maybe Chloe wants to pursue a more stable life while Beca is all about taking risks in her music career. This disparity in their future plans might lead to a break - up.
Perhaps their daughter has a special talent that gets her involved in a dangerous situation. She could be a prodigy in computer hacking, and while trying to help her parents on a case, she uncovers a secret that puts her life in danger. Castle and Beckett then have to race against time to protect her while also solving the case.
In a fanfic like this, there could be a lot of emotional turmoil. Beckett and Castle might start to realize how much they actually rely on each other. When they are pretending to be separated, they could find that they miss the little things about each other. For instance, Castle might miss how Beckett always has a smart comeback during their banter, and Beckett might miss Castle's goofy sense of humor. This could lead to some internal conflict for them as they try to maintain the facade while also dealing with their growing feelings for each other during this 'pretend' separation.