[Warning: The following contains spoilers for The X-Files' Season 11 finale]

The X-Files said goodbye to Dana Scully (Gillian Anderson) on Wednesday.

With Gillian Anderson previously revealing this season would be her last playing the red-headed skeptic, the Season 11 finale marked Scully's final appearance in The X-Files. And with the show's future up in the air (Season 11 is averaging a 0.96 rating in the 18-49 demo versus Season 10's 3.2), it's possible Wednesday's episode will also act as a series finale, meaning this might be farewell to all of our beloved X-Files friends, Mulder (David Duchovny) included.

With that in mind, the stakes were high going into "My Struggle IV," the conclusion of the ongoing mythology that began in the first revival season. With their son William (Miles Robbins) on the run from The Cigarette Smoking Man (William B. Davis), Mulder and Scully track down the powerful teen in the hopes of protecting him from Mulder's diabolical father. However, it's actually William who protects Mulder and Scully, using his abilities to trick the Smoking Man into shooting him under the belief that he was killing Mulder. This gives the real Mulder the opportunity to shoot and (presumably) kill the Smoking Man, who falls into the nearby ocean and floats away.

Mulder and Scully then grieve for William, whom they believe to be dead but is actually secretly alive. During the discussion, Scully reveals to Mulder that he was never William's father, biologically at least, and adds that she was never a real mother to William either. But now, Mulder and Scully have a second chance to be the parents they never were to William because DANA SCULLY IS EFFING PREGNANT.

It's a lot to process, particularly in light of the show's uncertain future and Anderson's departure. And so TV Guide went straight to the man behind The X-Files, creator Chris Carter, to discuss the finale's biggest twists and cliffhangers, as well as get his thoughts on where the show goes next.

When and why did you decide you wanted to end the season with Scully being pregnant?
Chris Carter:
It was my plan since last season. I had this four-part mini-series within the series, what we're calling the "My Struggle" series, and I wanted to play with the question of William's paternity, I wanted to play with the question of Mulder and Scully's relationship, I wanted to play with the science that we had previously established. This was all, for me, of a piece and as you see the puzzle pieces fit together in the season finale.

Scully has always played the skeptic role in the series, but her pregnancy is a real miracle. How does this shift Scully's — and also Mulder's — perspectives on faith and belief?
Carter:
Well, the idea that a woman who, in the series, is 53 years old getting pregnant is not outside the realm of extreme possibility... But because of Scully's previous miraculous pregnancy and birth and because Scully has alien DNA, we have to take it as an X-Files moment that she's going to be pregnant again.

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Scully was very happy to share the pregnancy news with Mulder, but the entire episode leading up to that was extremely dark. When the show originally introduced William all those years ago, did you already know that his storyline would ultimately lead to such a deadly showdown?
Carter:
There have been so many twists and turns. As I tell people, it was interesting with the mythology that for about the first five years we were making choices. And then because you had made so many choices and you had gone in so many directions, many of the choices started to make themselves. And then the mythology, in a way, demanded its own trajectory. And I think that, for me, it is kind of a beautiful arc that has lasted over now 25 years.

Did you ever consider having William actually die?
Carter:
I wanted people to fear that he had died, but I imagined him as you see. What does he have? What does Mr. Y tell him? He has what everyone wants, which is immortality.

How does the fact that the Smoking Man thought he was killing Mulder when he allegedly killed William weigh on Mulder?
Carter:
It freaks Mulder out. Mulder's dealing with so much at that point. He's reeling and he's trying to put it all together. Could his father have killed him? Did his father kill his son? Is it his son? Mulder's probably feared all along, and certainly William intimates as much in the hotel room, that the connection between the two of them is maybe not as biological as Mulder might have imagined. So he's processing all of that as he stands there looking into the dark water.

We've seen how much Scully, in particular, loves William and has tried to protect him for his entire life, so why does she say that she was never a mother to William after his apparent death?
Carter:
Well, she says she bore him, she carried him, she tells the story. But she was never a mother to him because she gave him away. So motherhood is two things, it's both birthing someone and raising someone, and she really never raised William.

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What do you think Scully and Mulder will take away from their experiences with William that they'll apply to this second chance at parenthood?
Carter:
I'm right with them. I'm standing there at the end of that dock wondering, "Now what?" So I can't give any clear answers. I have ideas, but I haven't made any decisions yet.

Can you confirm that the Smoking Man is, once and for all, really dead?
Carter:
Well, remember, he has access to science that only he has in his possession. If that was a rejuvenative science that allowed him to reappear at the beginning of last season, what is the effect of that science on him as he floats away?

The Smoking Man assumed Skinner (Mitch Pileggi) was dead after the car crash, but we never get confirmation. What can you say about whether Skinner is alive or dead?
Carter:
I'll say it's a cliffhanger.

Did you know this would be Gillian's last episode when you wrote the finale?
Carter:
I knew that she had, of course, said that and certainly that was on my mind. But this is where I wanted to end the "My Struggle" series, the four-part series I've been talking about. This is how I had imagined it would end.

Knowing that this will be the last time we see Gillian as Dana Scully, how do you feel about the way Scully's storyline comes to an end?
Carter:
You know, it's sweet but I don't think of it as an end. I think of it as a possible next beginning.

Kersh said he was shutting down The X-Files and taking Mulder and Scully's badges, so what do you imagine their lives and careers will look like moving forward?
Carter:
You remember, being a fan, that we shut down The X-Files at the end of Season 1. It's not the first time. It's really, for me, it's kind of part and parcel of the moment we live in. There seems to be no clear beginnings or endings. Everything is ever in play and I think that to be the same for The X-Files in this case. They're no closer to the truth than they've ever been.

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Where do you currently stand regarding the show's future without Gillian?
Carter: I haven't really grappled with that. Certainly, there are other people grappling with it on other levels, meaning the corporate level. Fox was just sold to Disney. I think there's so much that is unpredictable and unforeseen, as you'd expect of The X-Files.

Have you considered continuing the series through some sort of reboot or spin-off with a new central cast of characters?
Carter:
I haven't. That's not to say it couldn't be done. There could be prequels. I joke that there could be the Broadway musical.

Finally, I have to ask: What did Scully whisper in Mulder's ear in "Nothing Lasts Forever"?
Carter:
I can't tell you. It's funny that people thought she whispered she was pregnant, but if that were the case, Mulder's reaction would have been much different.

The X-Files entire series is available to stream now on Hulu.