There's a chance that he would lose his passion for writing. Beckett was often his inspiration, and with her gone, the joy of writing might disappear. He would be so consumed with grief and thoughts of her that he simply can't focus on creating stories anymore.
Castle might become obsessed with finding the truth about what happened. His writer's mind would start formulating theories and he would stop at nothing to get justice for Beckett, which could put him in dangerous situations.
He could become more withdrawn. Losing Beckett like that would make him hesitant to let people in again. He'd be more guarded, fearing another loss.
One challenge could be the state of the body. If it has been damaged or decomposed, it would be difficult to identify. Another might be the lack of proper identification tools or information at the scene. Maybe there are no fingerprints available or dental records are missing.
He would likely feel extreme shock. Just the sight of her body could send his mind into a tailspin. He might also be in denial at first, not wanting to believe that it's really her.
Castle could initially deny it's her. He'd look for any sign that it's not Beckett, checking for details that are off. As he realizes it is her, he'd break down, crying uncontrollably. His world would shatter because she was such an important part of his life, and he'd be filled with regret for any unsaid words or things they didn't do together.
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.
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.
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.
It could be a vengeful criminal that they put behind bars. This person has escaped and wants to get back at them, so they engineer their disappearance. Maybe they have a whole elaborate plan to torture them in some remote location.
He could react with anger. After all, if he has feelings for Beckett, seeing her with someone else like Vaughn might make him furious. He might lash out at both Beckett and Vaughn without really understanding the situation.
There could be. The Castle fandom is quite creative, and a pregnancy plot for Beckett is a popular trope in fanfiction. Some fanfics might focus on the romantic aspect of it, with Castle being over - the - moon and taking extra care of Beckett. Others might explore the more practical and challenging sides, such as Beckett still trying to solve cases while dealing with pregnancy symptoms.