We first see the mysterious Mr Smith in Rise, when he opens a package sent by the late Captain Montgomery containing case files relating to Johanna Beckett and John Raglan. As he puts in a call to the Capitol and then to Castle, we realise that now, after Montgomery's death, he has become the man to hold the evidence that has been keeping Beckett and Montgomery's family alive. He instructs Castle to look after Beckett and steer her away from investigating her mother's murder.
In Dial M for Mayor, Mr Smith reappears to warn Castle that the death they are investigating relates to Johanna Beckett's murder, and gives him a phone number. Castle eventually calls to meet him, and they rendezvous in an underground parking garage, where he confirms that the murder is indeed part of a plot to topple the mayor. In a second rendezvous after the case has been solved, Castle demands more answers of Smith, but Smith refuses to give them. All he will say is that he intervened to save the mayor because he guarantees Castle's presence with Beckett at work, and that "a well-placed pawn can be more powerful than a king".
At the end of Always, Cole Maddox, who has escaped after throwing Beckett off the roof of the hotel, tracks down Mr Smith and demands the evidence he holds on Maddox's employer, because it's time to but Beckett in the ground once and for all.