Due to the fact she is away from her new fiancé and that also now he is dying after being affected while he was kidnapped in the first episode of the sixth season. Rachel her new partner and Kate think that the Defense Secretary has something to do with the affection of Castle among them.
The person who took Castle hostage died from it in the first episode of the sixth season. It is a race against time to save Castle and prevent another outbreak.
Pi is not annoying as some people claim he is. He may be dim witted but not as worse as we have seen characters in previous seasons.