SPOILER ALERT: Do not read if you have not yet watched “Utopia,” streaming now on Amazon Prime Video.

For the first season of her Amazon Prime Video adaptation of Dennis Kelly’s original U.K. drama “Utopia,” Gillian Flynn wanted to end on “one of those old-fashioned cliffhangers” in which the audience would be wondering, “How can our hero possibly get out of this?” she tells Variety.

And she succeeded whether you think the hero of the story is Jessica Hyde (Sasha Lane), a young woman who was raised in a secretive facility, treated as a lab rat, and became the central character in a comic book also called “Utopia”; one of the nerds (as Flynn affectionally calls them), a rag-tag group of fans of the comic who first met online and then got pulled into the very real conspiracy hidden with the book’s pages; or even Dr. Kevin Christie (John Cusack) himself, the man behind the not only Jessica’s early days of medical experiments, but also a plan to sterilize three generations of people in order to stop overpopulation.

Although Christie was revealed to be Mr. Rabbit, the nefarious man the comic-within-the-show warned its readers would bring down humanity, his plan came with seemingly altruistic intentions. And by the end of the first season, a new threat emerged in Milner (Sonja Sohn), a woman who was once partners with Christie but who had separated from him due to a difference of beliefs.

“If Christie’s theory of life is free will and we just need to slow down the population and stop each generation from handing down the previous generation’s prejudices and nastiness, and really reteach this new generation how to value being good humans, it’s a nature versus nurture thing. Sonja’s character says, ‘Humans will always find a way to be s—-y. That’s just how we are,’” Flynn says.

As the first season unraveled the mystery to reveal Mr. Rabbit’s identity, as well as the extent of his true plan, events along the way tested allegiances within the core group, resulted in some deaths (RIP, Sam), some near-deaths (sorry about your neck, Becky) and a major betrayal (Wilson Wilson, of all people, how could you!?). Things were not any simpler on Christie’s side of the story, either, as arguably his most-trusted assassin Arby (Christopher Denham) ended up giving him up to the group and, seemingly unbeknownst to him, Milner has struck out on her own.

Not every loose thread was tied up or question answered in the eight episodes of the first season. But that was by design, Flynn says, because “unlike everything else I’ve done, there could be a Season 2, so some things can land more gracefully with a Season 2.”

Here, Flynn talks with Variety about some of the unanswered questions, inspirations behind the visual look of Home, Dr. Christie’s ultimate plan and what to expect from a potential second season.

The show leaves Jessica in a pretty precarious situation for a number of reasons. What is the biggest threat to her or complication for her going forward?

Oh you’re asking questions I’m not sure the answer to! It would be hard for me pick what all she must surmount. Obviously Dad’s going to come into play and we’re going to learn more about Milner. We’re going to learn about the Milner-Christie-Dad origin story. The mythology I have all figured out.

What went how you chose to reveal that Jessica’s father is still alive — and drawing new comic book pages?

I want the audience to be debating about it, I guess, a little bit: Is Dad being kept down there against his will by Milner or is Dad being kept down there for his safety because of Milner? I wanted to play with that at the end — that you would see him. “I have your daughter,” and you can debate whether you believe that that is a reassurance or a threat.

Early on in the season, you killed of Sam (Jessica Rothe), but later it appeared Becky (Ashleigh LaThrop) had also died, only for her to wake back up. How did you determine who to kill and who to save?

I will admit Sam was a character created partly in order to kill her off — I will fully admit she was always slated for death. Jessica Rothe was so good I really had debated, like, “Maybe she has a twin or something” because she was so much fun to work with. But I liked that idea of the person that you think is going to be the leader — and you could really probably play a drinking game in the first two episodes of the number of times where Sam knows the most, Sam’s the leader — and killing her off. Obviously that’s not new; I remember seeing “Psycho” when I was a kid and being completely shocked when Marion’s killed. To me that was a sign of, no one’s too precious here in this world. To me, it showed that idea of how fungible that life is. To Jessica, she had this place to go as she slowly — very small baby steps — starts understanding and mildly, at least, valuing human life.

And I liked [upending] the idea of the blonde-haired, blue-eyed girl, who as we’ve so often been taught is the one who’s going to survive in horror movies. Certainly Jessica Rothe has made her name in that great one, “Happy Death Day.” And instead, she’s killed off by Sasha, and it’s like, “No, no no no, new world order, folks.”

In the beginning, learning Jessica Hyde was a real person and getting to meet her could have been enough for these characters to follow her. But after Sam, did you feel Jessica needed to do anything to earn being followed as a leader?

There was definitely a conversation about that: “Will people come back after that? Will people be able to accept Jessica? Will they want to see her only punished?” To me, it gives a little bit of a self-selection factor to it. I remember “House of Cards” when he, right at the beginning, kills the dog, and it’s like, “This is the show you’re signing up for, and if you’re not OK with this you might want to just switch over to the Hallmark Channel.” So to me, this was the world where you are, and I wasn’t going to worry. If you’re offended like that, if you don’t like that, the rest of the show is dark and it might not be the show for you. It was the same thing when I was writing “Gone Girl”: I had a conversation with my editor where she was like, “I just want to check in with you because you’ve written a book with two unlikable main characters and it’s a whodunit where you find out who done it smack in the middle, and it has an end where justice is not necessarily served.” And I was like, “Good point, yes.” But to me, I couldn’t even worry about that. I didn’t think it would be right to make Jessica do good deeds or whatever just so you’d stick with the series and over the course of each episode figure out who she was and why she was like that.

But from a character perspective, do they have to like or trust her, or do they just have to follow because they don’t think they have any other options?

Becky and Ian have that conversation at Grant’s house, where Ian was like, “She killed our friend,” and Becky was like, “I know and it makes me feel horrible but I want to live.” Each of the group has different reasons: Becky stays because she wants to live, Ian stays because of Becky, and Wilson stays because he’s like Jessica, just without the violent part.

Well, at least in the beginning.

Yeah, he wants to find what happened.

Speaking of Wilson Wilson’s willingness to be violent at the end of the season and his betrayal of the group by joining Christie and taking Becky, was that darkness something you felt was in the character all along and was just awoken in the finale, or did the experiences he had change him?

I’m trying to be careful about how I speak because I never like to tell people how to feel about certain characters, but for me the idea was that Wilson is a very pragmatic person who’s spent his life with these convictions and this belief system that he prides above everything else, and possibly in the place of human relationships. And as Christie’s speaking to him, what he says rings true so he gets to this point where it’s, “Do I side convictions? Do I side with the heart?” And so it comes down to that kind of decision, I think.

I assume when you wrote the scene revealing him in the car with Christie you had made a decision as to whether he was with him because he truly switched sides or had a plan of his own up his sleeve —

No, I have not. I’m not sure if that was wise of me to answer. In that moment he is following his convictions, but it’s one thing, when your friends aren’t around you, to make that choice. And I think when he’s now faced with Becky at the end and seeing the flesh and bone of the reality, what happens then?

What does happen then? Did any performance choices Desmin Borges made in that scene chance what you want to come next for Wilson Wilson?

I don’t think so because in the moment he’s very genuine. So to me, no, I’m not worried about that.

Were all of the clues that Wilson taped up on his wall real things that led to Mr. Rabbit, or did you throw in any red herrings for him as a character or the audience who might freeze-frame and try to figure it out too soon?

I think that they’re all real. I’m pretty sure they’re all real. A couple of the diseases we played with a little bit more. I think we might have invented one disease maybe, or expanded it.

Looking at Christie’s side of the story, were there pieces of the science behind the viruses and his idea for sterilization in vaccinations that you had to write specific to how healthcare is handled in the United States, versus in the U.K., where the original series was set and aired?

Certainly I wanted it to feel political. I wanted the protestors and it to feel like a thing that people had a big reaction to. But as far as the pure medical procedural pieces of it, that wasn’t something I overly worried about because I was very deliberately not doing a medical procedural pandemic story — that was just one plot point. So we had an advisor who could say, “This is what a hot zone looks like; this is what would happen.” My questions were I was always not “would this happen,” but more like, “could this happen” so that I had as much leeway and if I was breaking real, actual rules, I at least knew that I was. Sometimes it was like, “Well, for the storyline I don’t have three weeks — the way this would play out in a real time or that type of thing.” But I wanted it to feel not so far out that you were taken out of the story and crossing your arms while you’re watching.

Were there lessons learned from the research process of this show that you think apply to the real-life pandemic we’re facing now?

No, and a lot of that was by choice. I wanted to be clear that we weren’t doing any pandemic procedural. It’s not “Outbreak”; we’re not giving the sense of what always happens during that kind of emergency. I wish we’d figured out social distancing! We did not know about social distancing when we were filming. Of course now, I look at [scenes] and I’m like, “Stay six feet apart!” But for the most part, when you see someone quote-doing science, that’s literally what it is: They’re quote-doing science. They’re not solving a pandemic.

Christie’s plan to reduce the population with this sterilization is supposed to spread throughout three generations, but how can he really control it so that there are still people left who can reproduce and continue to keep humanity alive?

The idea is that not everyone’s going to get vaccinated. And the idea is that certain ages are going to go first and each generation would receive the actual working doses mixed with the population doses, so that it would he could control how much each generation had. So his plan is not to completely depopulate the Earth.

But even the best plans can go awry. And immediately, the next thought for many was likely, “How much is he controlling what groups or ethnicities get which doses?” Is this a situation of him wanting to create and American society in a specific image ala eugenics?

The short answer is no because as you see when you go to Home he’s all about equality among gender, among race — that’s his whole plan. So no he is not remotely doing any sort of eugenics.

At Home there was equality among test subjects, but they were test subjects and ultimately being treated as expendable lives, from giving them purposes as drug testers to martyrs. What were your inspirations for creating what Home looked like — especially considering Jessica remembered it as an actual home, but the comics and other people in her life kept pointing out it was a prison?

It was a big question of how much we show Home and how much we save for and hopefully get into in Season 2 because it fascinates me. My thought was, Home has to be a place without technology, No. 1, for purely pragmatic reasons — so that no one can find out what’s outside of Home. And we see the school room a little bit and that everyone’s in a version of a uniform because we want equality, and so we don’t want one kid has better sneakers than the other or something like that. But at the same time they have their color options so they can express themselves. So I had a lot of conversations with everyone from costumes to set dec about what it would look and feel like. It is that feeling of playing old-fashioned games — not like they’re playing 1800s house or anything like that, but it all comes from Christie’s vision that he really believes you should play games of cooperation, not competition. Anything that goes towards equality and good citizenship is what I wanted it to feel like, so children have their chores and are involved in growing their food. We’re a big Montessori family, so it’s that mission on acid. And originally I thought we’d see more of it, but I’m hoping in Season 2 we really get into it.

Hidden details and Easter eggs was such an important part of the story the characters were digging into within the comics. What was the approach to such things in the show itself, such as the “Gone Girl” musical on the marquee?

A lot of it was just for fun, but when it was stuff like that it was because we couldn’t get name clearance for everything. Hilariously we had tried eight different musicals for that dang billboard and then finally we’re getting down to it — we have to put it in for VFX — and I’m like, “I know who can give us the title!” So sometimes it was last minute fun, sometimes it was getting a character named after a friend or the crew. My kids and my whole family are in it.

And you’re in it!

I’m in the subway, I’m checking into the hotel in Episode 1, and I give Rainn [Wilson] pancakes in another. So we fully embraced “Spot the Creator,” that old favorite game. And that’s my daughter sitting on my lap in the subway. And when they’re at the big mansion that has the coat of arms, and it’s like, “Oligarchs are never home,” the picture of the guy in full royal dress is our location scout. He’s from Bulgaria, and he was like, “I must have this.” We got a portrait of him, which I hope he receives.

In the first season there were certainly times the audience knew more than the characters, but there were plenty of big moments to keep them off-kilter. What is the key to maintaining that tone going forward?

I have an interesting relationship with when the audience knows versus when characters know, and to me it’s not a rule, I feel like it’s more situational — because sometimes I like a good surprise and a twist and a shock, where it does come out of blue as long as it’s been earned and you can go back and and see that the seeds are there. But sometimes I think there’s a lot of joy to be had in seeing a general decision made and then getting to see the machinations of that coming to fruition. Getting to see Thomas in action, spinning the whole death of Dale, for instance, there was a question [about] maybe we should see it happen so it’s more of a shock? And I was like, “No, to me, I want to see what is the target and how does that.” And certainly, again, it’s like “Gone Girl”: you know in the middle what Amy’s done and then you get to play with her for a little bit. It’s which is more gratifying.

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