Adult Fear: A Serial Killer who gains people's trust and takes their little daughters from their beds? He does God knows what with them, kills them and takes a twisted souvenir. And he thinks he's re-enacting Alice in Wonderland. It cannot get much scarier than that.
Alice Allusion: Roche's victims were little girls. He collected cloth hearts from their clothes and kept them hidden in a copy of Alice in Wonderland. The phrase 'Mad Hat' appeared in Mulder's dreams and also as a mark near a newly found crime scene. Roche used to live on Alice Road in Boston, and Mulder concludes that that's how he first got the idea and that he took the role of the Hatter.
Bad Dreams: Mulder's nightmares haunt him in this episode.
Call Back: In "Nisei", Mulder lampshaded that he got tired of losing his gun and pulled out a back-up gun from his ankle holster. Mulder's back-up gun is very important in this episode.
Scully's line, "You said yourself once that a dream is an answer to a question we haven't yet learned how to ask," is a call-back to season 2's "Aubrey."
Catapult Nightmare: Mulder falls asleep in his office by the desk and he wakes up gasping "Samantha!" while flinging himself up.
Chekhov's Gun: Literally a gun. When Mulder and Scully go to the prison through a metal detector, they put their guns into a drawer. Notably, Mulder takes off two guns, one of which he carried in his ankle holster. Later in the episode, Roche escapes with Mulder's weapon... and he is killed with the back-up one.
Continuity Nod: Reggie Purdue, Mulder's former boss from the Violent Crimes Section and his friend who appeared in "Young at Heart", is mentioned again. It was he who brought Mulder on this case as he rightly thought that Mulder would get into the killer's head.
Numerological Motif: Roche originally said he had 13 victims. When his trophies are found and there is 16 of them, he says it just seems more magical.
Paedohunt: John Lee Roche is a very disturbing child molester. Paedophilia is a horrible kind of evil.
Police Brutality: Mulder gets frustrated while he interrogates Roche, and hits him very hard in the jaw. A guard walks in, surprised, but when Roche complains, he says he didn't see it. Scully is visibly upset but doesn't report it. Mulder still has to account for this action, though, because it was videotaped.
Prisons Are Gymnasiums: Roche plays basketball in a huge hall. His other privileges include access to the prison's library with the Internet.
The Profiler: Mulder's brilliant profiling skills play a very important part. His profile helped to catch Roche in the first place as he was able to conclude how he thought and what he did.
Psychic Link: Mulder thinks that Roche can get into his head and that they share some kind of disturbing connection.
Recurring Dreams: Mulder keeps having a dream about a park, and that's how he finds one of Roche's previously unknown victims buried in a park. He also keeps dreaming about Samantha's abduction, which is vaguely similar to his old account of it as he remembers it from a hypnotic session. A red laser light beam keeps appearing in his dreams, forming words, messages and pictures.
Reminiscing About Your Victims: Roche reminisces about some of his victims and how he tricked their parents into trusting him. He tries to convince Mulder that his sister Samantha is one of them. It turns out she wasn't. He's just a jerk and enjoys tormenting him.
Serial Killer: John Lee Roche, a murderer and child molester of little girls, playing some sick and twisted version of the Hatter from Alice in Wonderland.
Mulder received the first speech for hitting Roche in the prison.
Scully was reprimanded, too, because she hadn't reported him. However, she was really pissed at Mulder herself as she is so fair-minded that striking a prisoner who cannot fight back really bothers her.
Skinner tells Scully that she let him down as she promised she would keep an eye on Mulder and make sure he's not going to do anything crazy. Skinner, you should know better by now, there is no stopping Mulder from that.
Skinner's second shout-down of Mulder was the most serious. He found out that not only had Mulder checked out Roche from the prison, it also turned From Bad to Worse: Roche got Mulder handcuffed, took his phone, his badge and his gun.
Skinner: Where's your gun? How do you explain yourself, Agent Mulder? Mulder: I don't. Skinner: You don't. A predator is loose because of you. God only knows how many hours lead he's got.