#3 On top of causing her considerable pain, it will also literally take her "cool", her backup and partner away. Which could make her both an easier and a harder target to kill. Because it makes her unpredictable, which could make her more calculated because she's got nothing else to lose. But because of that, it could also make her act reckless and stupid, which we've seen happen a lot. That will make her easier to kill.
#2 But I think in 5x13 Bracken realized that Castle knows more than he thought he did and based on their interactions and the way Bracken observed Castle and Castle and Beckett together, I think he knows now that Castle and Beckett are a couple. And that Castle will do anything to keep Beckett safe. Which makes him just as much of a threat as Beckett. The fact that they're together also makes Castle both her strongest and weakest point, her achilles heel. Take Castle away and Beckett loses her support system. And Castle might not always be useful depending on how you look at it, but just his presence always is. Beckett feels safe with him, which allows her to think more clearly, make better decisions under pressure. Decisions that will keep them both safe. Take that away and Beckett is exposed, vulnerable.
Hi guys, just dropping by. @Tonya, I think at first he wanted to keep her from finding out who he was, that's why he wanted to kill her in the first place. He knew enough, based on the fact that Beckett killed Coonan, and was hunting for him, Bracken, that if she found him she might try the same with him. It's kind of like squash the threat before it becomes one. I think with the other people, Castle, Martha, etc, it's different because he's not actually sure that they know anything and if they would even care.
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