[Warning: The following contains spoilers for The X-Files' latest episode, "Ghouli." Read at your own risk!]

After all the teases, speculation and build up, The X-Files re-introduced Mulder (David Duchovny) and Scully's (Gillian Anderson) son William in Wednesday's episode.

When the agents investigate a case in which two teenage girls attacked each other thinking they had each been fighting a creature known as Ghouli, they quickly discover the case is far more complicated than they ever imagined when they learn both girls had been dating Jackson Van De Kamp — a high schooler who shares the same last name of the couple who adopted William all those years ago.

Unfortunately, before they can speak to the young man they believe may be their son (played by Miles Robbins, Susan Sarandon and Tim Robbins' son), the teenager and his parents are fatally shot — or so it initially seems. In actuality, Jackson, aka William, has developed his powers to the point where he now has the ability to create false realities and make people see things that aren't there, such as Ghouli and his own dead body. Using these abilities, William takes the opportunity to go on the run before the government men hunting him can find him again — but not before sharing a tender moment with his birth mother.

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TV Guide spoke with X-Files icon James Wong, who wrote and directed "Ghouli," to get the inside story of William's return.

What were the talks like with Chris Carter about this episode and how he wanted to re-introduce William?
James Wong:
I'm really interested in the William story from the last season, so I knew I wanted to touch on that. And this time, when we talked about it, we wanted to explore the possibilities of a near-miss kind of meeting, which he was really into as well. I think one of the things Chris said when we first began talking about it is that he really didn't want them to connect face-to-face, or face-to-face in a way that's like, "oh, here's my son." Nothing like that. So the challenge [was] to think about how to do that, achieve that and then have a satisfying connection. And I had this crazy sleep paralyses episode happen to me in Mexico, so that's kind of how it all came about.

This is the first time we actually get to see what William is now. What were the main tenants of his character you wanted to get across?
Wong:
One thing that I really was interested in is showing his abilities... I was interested in what that meant in terms of how he interacted with his world. But also, I wanted to actually understand that Scully [putting him up] for adoption didn't wreck his life in a way. I wanted his adopted parents to have been a positive force for him even though this whole tragic thing happens. So those were a couple of important things to address.

One of the first things we learn about William is that he almost got both of his girlfriends killed as part of a cruel prank. What does that say about William and how does that color our interpretation of him?
Wong:
Well, for me, the interesting thing is that you didn't know. It was a horrible prank gone wrong and for me, you didn't know that it was him who had done it. So I feel like in a way I'm cheating a little bit in that we don't quite know that he is the culprit, so you get a chance to not judge him so much until later when you find out. But I do think that in doing that, it sets up what he's able to do and what he's capable of in the later episode where we meet him again. I can't say too much about that because that's sort of the end of the season, but I think it informs us that he's not a person to be trifled with.

My favorite part of the episode is Scully's monologue that she delivers to William's body when she believes that he's dead. Can you talk about writing and directing that scene and what you wanted us to see in Scully in that moment?
Wong:
Gillian and I talked a lot about that scene. She was really interested in how to portray that as a mother who felt like she did the right thing but at this moment feels that it was maybe completely wrong, and that failure is something that she was interested in exploring for herself and for Scully's character. So when we started working on it, part of it is that she felt this dichotomy between knowing whether this was William or not and not knowing, and whether she was apologizing to a corpse that is not her son. But in the end, she had to just kind of open her heart and say what she really felt about what she had to do. And that way, it was obviously how she felt the entire time. But the other thing that was interesting, I thought, was that Gillian really wanted to have that moment when William's body disappears, that Mulder and Scully have a different idea of what's happening there. Whereas Mulder is thinking all these reasons why the body disappeared, she actually has a glimmer of hope in that moment. She was really interested in playing that and dealing with that.

William heard everything Scully said in that speech. What does he take away from her words and how deeply do they affect him?
Wong:
I really wanted him to not feel like his adoptive family was not a family, so I think it's interesting. I have an adoptive child myself so I was kind of thinking of what that would mean to my daughter. For him, he's got to be kind of removed from the emotions of it at that moment because he had this tragedy happen to his parents and then to have this other person to come in and say all these things which you don't quite know how to process in the moment, I think that's how it felt like. He has to wait and see until the end of the episode when he has a chance to really talk to her, even though it's in the guise of the author, the pick-up artist guy. He's still kind of feeling out that relationship.

When William and Scully do have that last chance to talk at the end of the episode, the last thing he says to her is "if you don't stand for something, you'll fall for anything." What message was William trying to get across to Scully?
Wong:
I think he's trying to say to her what he's about to do himself. I think he is sort of foreshadowing his character for the rest of the season, for when we see him again. It's a call to arms a little bit. I can't reveal anything other than that, but it's a strong statement. This is not a person who is just going to go away and disappear.

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Throughout this entire episode, Scully is more visibly affected by everything to do with William and Mulder seems more focused on just supporting Scully. How are we supposed to interpret Mulder's behavior and where his priorities lie in this episode?
Wong:
I think Scully had much more of a connection to William than Mulder did, even from the get go. She orchestrated the whole thing in the past with the adoption and keeping everything that happened a secret from him, as well. And so I think, for me, I think it's right that Mulder's connection to him is actually Scully versus his son, whom he doesn't have much of a physical or otherwise connection to. It was only really until the moment when Mulder is talking to Skinner that I felt like he reveals his grief about it... So I think she's much more affected by it in every way. In a way, that represents mothers' and fathers' connections to their child. The mother has such a strong bond from just through the pregnancy and carrying a life inside you. I guess that's what I was kind of going after.

This season started with the shocking reveal that Mulder isn't William's father and it's actually the Cigarette Smoking Man (William B. Davis). How do you think this horrifying truth influences the way we watch and interpret the family dynamic between William, Scully and Mulder play out now?
Wong:
I don't know because everything that the Cigarette Smoking Man says can be a lie. And to be honest with you, I didn't have that information until after I wrote the episode. It wasn't a thing where I go, "ah, this is what I need to do." So I don't know. To me, I didn't write the episode differently because of that because I didn't even know about that. I mean, I sort of knew about that, but I sort of didn't take it into heart, you know? To me, Chris and I never discussed it. It wasn't a thing like that. So I don't know. I didn't take it to heart. That's my honest opinion.

The X-Files airs Wednesdays at 8/7c on Fox.