[This story contains spoilers for the Jan. 20 episode of Counterpart, "Twin Cities."]

Counterpart creator and showrunner Justin Marks directed Sunday's episode, his first time helming an episode of the show (and his first time directing, period).

He did not give himself an easy assignment.

The episode, "Twin Cities," depicts the origins of the parallel world the series inhabits along with the origins of Management and the ways the two worlds started to diverge. J.K. Simmons and almost all of the show's regular and recurring characters are absent, save for a few present-day scenes between villain Mira (Christiane Paul) and Yanek (James Cromwell), her father.

Instead, the episode spends nearly all its time with a younger Yanek (Samuel Roukin), who's on the verge of defecting from East Germany to the United States when he accidentally creates the Prime world, then recruits several fellow scientists — the group that will become Management — from both sides of the Crossing to explore and experiment on the two worlds.

Things go badly awry when, following a small change to the Alpha world, East German police come to arrest Yanek's teenage son for distributing subversive materials. The boy has a seizure and dies — but survives on the Prime side. A grief-stricken Yanek begins crossing over and eventually kills Yanek Prime, setting a path to the paranoid world(s) Counterpart now inhabits.

"It was a monster of an episode," Marks told The Hollywood Reporter. "We planned for it all season long in terms of how we were going to have the money to shoot this episode in the way we knew we wanted to shoot it, and to have the time. The first feature film I worked on, an independent film, shot for as many days as this episode of television did. It was a big challenge, and I just kind of embraced the fear by preparing for every detail and every contingency.… That was the only way I knew how to counter the anxiety."

Marks spoke to THR about the concept for the episode, why now was the right time for it and where the show goes.

In creating the show and the world, did you have this level of detail in mind about how the Crossing came to be from the get-go, or did it fill in more as you went along?

We kind of always knew this is how it went down, and this is the story we were going to tell about the creation of the Crossing. There were some specifics in the details that started to evolve as the first season was finished and the second season went on.

The best example of it I can think of is we were so taken in the writers' room by the performance of Christiane Paul as Mira in the first season that we really decided to embrace her as a character and elevate her in stature, and kind of tie her origins into the origins of two worlds as it related to, in this case, her father and the way she was really the first experiment that had been done as a result of the existence of two worlds. Beyond that, we really always knew we wanted to tell this story in this long-spanning format that told a passage of time and began to differentiate these two men — who are so identical that it really doesn't matter which one is which and which world is which at the very beginning, but who then start to peel off from each other.

It struck me as almost a visualization of what might be on your writers' room board and all the branches it could lead to…

Yeah, which way it could go and how that would work. The split-screen format, we tried to use kind of sparingly, but introduce it in a way that would manifest that branching as it happened. It was something we originally conceived for in the first season. We thought there might be a time where we'd see the departure of Howard and Howard Prime [Simmons] through that means. But eventually we just told that story in words in the fourth episode of this season — how they treated their father differently at a key moment in their lives. But I always thought split screen is such a fun technique that at some point it would be fun to do it that way.

This is your first time directing, right?

Yes. I had never done it before. But this was a crew I knew very well and trusted. I didn't think I was ever going to do it, to be honest. I was focused on what it is to run a show and what it is to write everything and put it all together. I wrote the episode because I knew just for personal reasons I wanted to be the one to write the first draft of the origin of the Crossing. It wasn't until after writing it that I started to realize this would be the kind of episode I wanted to take all the way home. The studio and network were very supportive of it.

More than anything, I went to the crew and started to talk to Thomas Boucher, our first AD, and [Tobias Datum], our DP, and say "What do you think if we did this?" It's such a strange situation to be running a show and directing, because you're kind of your own boss in a very [laughs] awkward way. But they were all so warm and enthusiastic about the idea that at no point did I ever feel like I was in it alone.

Did you have physical doubles on set for the Management characters as well as using visual effects?

We've learned a lot of tricks over the last two seasons — and this was the final episode to shoot in season two. So after doing 19 episodes of a show with counterparts, you start to learn what works and what doesn't. Then you start to challenge it. With [the two Howards], we used John Funk, who's an actor as well as a close look-alike [for Simmons] to act opposite J.K. In this case, we had an actor by the name of Gary Reimer who was a close look-alike to Samuel [Roukin], who played Yanek, and could also act against him. So we used that, and even more so than with John Funk and J.K., there are shots that are entirely Gary when he's walking through the scene, and he's able to approximate Samuel's behavior so well that you don't even know it.

And then in other scenes, we did the traditional split-screen replacement. The other thing we wanted to experiment with this one, that I've always wanted to do, is twins. We cast in the Management group two sets of twins: Gregory and Lawrence Zarian [behavioral expert Volker] and Sarah and Laura Bellini [environmental scientist Ilse] to play counterparts onscreen with each other in a way that kind of took the pressure off our shoot days. It allowed us to sometimes shoot counterparts without having to do a split screen and do a walk-off. That was a really nice thing.

The scene that was the most fun for us was there's a moment when Management starts working together set to a needle drop, which was a conscious choice to step outside our traditional tone. There's a geekiness to the way these scientists work, and we wanted to convey the exuberance they had for each other. But it's all a single, uninterrupted Steadicam shot…as you move through the lab and see Management working.

In order to do that, we made close use of our two sets of twins, but we also had three actors who didn't have twins. We used body doubles and had a set with multiple hidden exits all around, so when the camera turned away, they could run around behind the camera, do a quick change into a new costume and show up in the same frame eight seconds later as their counterpart. We meticulously rehearsed it and storyboarded it with action figures to get it right. We wanted to start to push the vocabulary of how we do counterparts on this show. But you can only do that when you have 19 episodes already shot.

Why tell this story at this moment in the series?

I think a lot of it is we never felt like we had a world that depended on an exact answer to why and how it all happened. In a lot of ways, as I think you can see, there's nothing particularly surprising [in the world of the show] about a physics experiment in the 1980s in East Germany that went wrong and somehow accidentally yielded this duplication and a bridge between the two universes. That's pretty straightforward. What was more interesting was what happened after that and how people reacted and how the Office of Interchange began to form.

In order to land the impact of that, I felt like we had to earn those questions and that curiosity from people. I don't think that curiosity is necessarily there after episode one. Our focus rightly should be on J.K. Simmons' wonderful performance and the characters he's playing and the slow unpeeling of the two sides of the same self. Once we stood on strong thematic ground, then we could start to look backward and fill in some blanks in a way that also allows us to look forward in the story.

To that point, the way you've built out the world this season has taken J.K. and some of the other key people away from the center of the show at times this season. How do you balance that while also serving the characters audiences know best?

I wouldn't see it as pushing people out of the spotlight as much as continuing to shed more light on characters we introduced in the first season who hadn't gotten as much attention. The key comparison I always use in my head is what we did with Nazanin Boniadi's character, Clare, in the first season by kind of marginalizing her for six episodes, only to reveal in the final moments of episode six that she's the missing piece of all the puzzles. The same thing happened here with Mira, in terms of understanding who she is and where she came from, and then of course James Cromwell's character, Yanek, filling that in and building to the understanding of the role he played in the opening of the universes.

Mira is the spiritual mother of Clare, and now we start to understand the way Clare came to be who she is by understanding the villain of the series in Mira. In the same way, Emily [Olivia Williams] has gotten a lot more screen time this year than last year, given that she was in a coma for the entirety of it. We always knew we were building to her waking up at the end of the season and then to tell the story of the Emily we never knew in season two. That's what Olivia signed on for and waited very patiently for.

When J.K. first came on to the show, he was very adamant, for practical as well as for creative reasons, that he didn't want to be the only two actors on the show. He felt Howard and Howard Prime are only interesting insofar as their story of identity is told against the bigger ensemble. So we spent the entire first season and parts of the second building out that ensemble to where a comfortable level is.

Where do you want the season to land with its final episodes?

We broke this season in two halves.… The buildup to the raid on Echo [in episode five] and the reveal of how Management ties into the very origins of the two worlds [was the first half]. In the second half, having all those pieces in place, we want to tell a complete story of the early days of the Office of Interchange and Management's relationship to it. And we want to, while not closing the book, close off a certain chapter in the Office of Interchange's life.

That endgame is definitely an important place for the show to go. Ultimately the show is this Cold War allegory, but there have always been, in our heads, other exciting places for it to go in the future, and we wanted to use the end of this season to tee up the next level of escalation. I will definitely say we'll get a lot of answers to the character questions about which self is the true self and where people are destined to end up. But for reasons I won't go into, there's going to be quite a large question mark hanging at the end of season two.

Where are you in discussions with Starz about the future of the show?

We're talking about it now. [Starz CEO] Chris Albrecht and I have sat down, and I've walked him through the plan of the third season, and everyone feels on the same page creatively. At this point, we're watching as the streaming numbers come in and getting a sense of what the audience and the appetite is. We'll make our determination from there.

Do you feel pretty good about it at this point?

I feel really good about the creative, which is the part I can control [laughs]. I was out a couple days ago with Harry Lloyd, who plays Peter Quayle and who's in town for some other work. We were kind of walking through what he knows is in store for his character in season three, and our heads were spinning with the possibilities.

This interview has been edited and condensed.