- One really wonders how the actors managed to keep straight faces during an exchange in the episode "Per Manum", when Scully is talking to Mulder about sperm donation:
Mulder: At that part, I'm a pro.
- From "Three Words" when the Lone Gunmen finally see Mulder after he comes back from the dead.
Frohike: You know, it's really not fair. You've been dead for six months and you still look better than me. But not by much. '(They hug tightly, Mulder laughs softly)
Mulder: Melvin. I'd be a whole lot happier to see you if you'd just take your hands off my ass.
Frohike: (Embarrassed, he lets go) Sorry.
- From "Empedocles." Mulder shows up at Scully's apartment and is slightly miffed that she was expecting someone else.
Scully (exasperated): Mulder!
Mulder (startled): What?
Scully: I was just about to get in the shower, but I was waiting for the pizza man.
Mulder: You got something going on with the pizza man I should know about?
Scully (confused): The pizza man?
Mulder: Correct me if I'm wrong, but you just said you were waiting for the pizza man to jump in the shower.
Mulder: (squints suspiciously)
Scully: Do you want to come in?
Mulder: Thank you.
- A few minutes later, after Mulder has non-subtly drawn her attention to a present he's hidden behind her sofa pillows.
Scully: Is that for me?
- That scene is doubly funny because it's the first time in the series Scully has ever thrown an innuendo at him unprompted—usually it's Mulder with the suggestive comments.
- When the pizza man does arrive:
Mulder (answering the door): Little Caesar, I presume? (Turns to squint suspiciously at Scully)
Scully: Hi. Just give it to the man with the funny look on his face.
- At the end of "Alone," Leyla Harrison asks a question that the fandom wondered for years: how exactly did Mulder and Scully get back home from Antarctica in Fight the Future? That answer? We never hear it, because Mulder and Scully are too busy bickering over what actually happened.
- There's a little one from Agent Doggett in this episode, too. Mulder and Scully come to the hospital to see Agent Harrison and they run into Doggett, who panics for a moment and automatically jumps to the conclusion that Scully has gone into labor.
- Earlier in the episode, Scully and Mulder get ready to attend Lamaze.
Mulder: Hey. Ready to roll?
Scully: Yeah, let me just get my keys.
Mulder: Hey, don't forget this. (holds up a pillow) Relax the back, breathe in, breathe out.
Scully: How do you know all these things, Mulder?
Mulder: I'm unemployed. I've got a lot of time on my hands.(beat) Oprah, I watch a lot of Oprah.
- Monica Reyes trying to emulate whale songs in "Existence" to put Scully in a relaxing mood for giving birth. The look on Scully's face is priceless.
- The final scene of the episode, while Mulder and Scully are admiring the baby.
Mulder: What are you going to call him?
Scully: William, after your father. (Mulder is touched. They share an intimate look)
Mulder: I don't know. He's got your coloring and your eyes. But he looks suspiciously like Assistant Director Skinner. (Both Skinner and William are bald.)