Star Trek: Prodigy Co-EP Aaron J. Waltke Deep Dives Into Season 2’s Star Trek Lore

Warning: This Interview Contains SPOILERS for Star Trek: Prodigy Season 2

Star Trek: Prodigy season 2 is a remarkable achievement of intricate storytelling and deep Star Trek lore overseen by co-executive producer Aaron J. Waltke. The Emmy-winning writer-producer applied his die-hard Star Trek fandom to what many fans feel is one of the best seasons of Star Trek ever produced.

Star Trek: Prodigy season 2 sees the young Starfleet hopefuls of the USS Protostar face a timey-wimey threat to the Star Trek multiverse and its numerous timelines. Helping Dal R’El (Brett Gray), Gwyndala (Ella Purnell), and their friends save the universe is a cavalcade of legendary Star Trek heroes like Admiral Kathryn Janeway (Kate Mulgrew), Captain Chakotay (Robert Beltran), and Wesley Crusher (Wil Wheaton). Opposing Starfleet is the reality-eating menace of the Loom, and an old adversary, Asencia (Jameela Jamil).

Screen Rant had the pleasure to engage in a deep dive with Aaron J. Waltke into the myriad Easter eggs and behind-the-scenes decisions of Star Trek: Prodigy season 2, from tie-ins to Star Trek: Picard to the shocking ideas that were left out of season 2 – but may find their way into a potential Star Trek: Prodigy season 3.

What Was Left Out Of Star Trek: Prodigy Season 2

Screen Rant: Before we talk about all the cool deep lore in Prodigy season 2, let’s talk about what wasn’t in the season. What are some of the story ideas you had to cut for whatever reason? I wanted to point out also that I was surprised that Dal being an Augment and having multiple abilities didn’t really factor into the season. That was something I was kind of waiting for, and I was like, oh, that didn’t happen.

Aaron J. Waltke: Well, first of all, with Dal’s Augment status, it was something that we obviously heavily featured in season one. And when it came to breaking season two, we realized that with everything going on with Gwyn being displaced from time, the search for the lost Protostar, the Loom, it wound up feeling like it would have been shoehorned in in a way that would have served neither story.

Just like in Deep Space Nine, the story of Odo’s heritage as this sort of unknown being eventually finding out he’s a Changeling, and then eventually, as the story goes on, you find out it’s part of the Dominion and the Dominion wants to conquer the Milky Way galaxy. We realized we didn’t have to answer every single thing and service every single thing in this season. And our hope, obviously, is that we’ll find a way to continue the story in some way, in which case we definitely will. As you’ve astutely pointed out, there are a few mysteries that are still surrounding Dal’s origins that we would love to explore.

As far as things that didn’t make it into the season, a lot of it is small things because, as you know, it’s so jam-packed wall to wall with story and lore and character and emotions. There are things that inevitably we had to leave on the cutting room floor. One of them was something I alluded to online. Ma’jel has sort of white highlights in her hair. And we actually likened that as being part of the sort of Vulcan elite status, something that I think we had previously seen in the character of T’Pau in “Amok Time.”

I believe Kirk even describes her as ‘All of Vulcan wrapped up into what one person.’ And we thought, wouldn’t it be interesting if here in the 24th century, there was somebody who was perhaps part of that house, distantly related or a direct descend, that had that kind of pressure of being the Vulcan-est Vulcan. And how would that affect someone like Maj’el, who’s still a teenager. As we know, Vulcan still feel, they just suppress it. And you get a little bit of that in the scene between Gwyn and Maj’el when she opens up about how she feels like she’s bereft of purpose because she’s no longer a member of this elite squad, the pride of her parents. She’s now sort of on this strange journey sent there by Wesley for some unknown purpose that she’s yet to be told. And so, you see that weigh on her a little bit in those episodes until she realizes that it’s just her presence throughout. It’s not about some grand gesture. It’s about who you are, on the whole of it.

A couple other ideas that had been left on the cutting room table. I think at one point we talked about trying to do a little mini-time loop episode with Jankom. We thought that would have been just some fun playing with time getting disrupted, especially in the back half of the season. But ultimately, we realized that it was kind of a standalone in what was becoming a heavily serialized wrap up of the season, and it probably would have felt a little out of place. As much as we wanted to have a Jankom story, we’ll get there, gang. We had some stuff with Jacob in this season, but we’d love to do a Jankom hero story.

At one point, I think we had discussed the possibility of what other universes can we explore? And I think at one point, we talked about trying to bring in even the Kelvin universe, but we just simply didn’t have time in the “Cracked Mirror” episode, where they’re going into all the different universes. And we were like, ‘Oh, what if we brought in that Captain Kirk, and he had to help them for a couple of episodes?’ It was a cool idea, but it was just a little bit too many sauces in the stew kind of a thing. I think it would have been fun. But I think it would have diverted from the story we were telling. It would have been the Captain Kirk show for a couple of episodes. Maybe that’s season three. We’ll find out.

Star Trek: Prodigy Season 2 Returns To The Mirror Universe

I love the Mirror Universe more than most. I find a lot of people don’t seem to dig it as much as I do. But I love this perverse, messed-up evil version of Star Trek. Prodigy showed Mirror Janeway and Mirror Chakotay. That’s now the farthest point in the late 24th-century Mirror Universe we’ve seen since Deep Space Nine. Did you have heavy conversations about what the situation is in the Mirror Universe now?

Aaron J. Waltke: Yeah, we did. You know, I love Deep Space Nine. It is my favorite of all the Star Trek shows for a few reasons. I’ve come to appreciate all of them almost equally, but that’s just the one I loved as a high schooler. I was well aware of where we left off with the Mirror Universe in that they initially were on their heels being attacked by the Klingon-Cardassian Alliance. But then, the last we saw of them in Deep Space Nine, they had successfully kind of repelled that advance, and it seemed like they were finally going to be able to rebuild their empire.

So in my mind, it seems unlikely that they would all just be good guys now. Especially because them making major reforms to their society with Mirror Spock ultimately, as stated in DS9, is what allowed their society to collapse and become vulnerable to the other outside forces. So we thought at least some faction would probably be like, ‘We have to go back to the old ways’. And that’s how we get the classic sleeveless shirts and the knives they have attached to their little holsters.

And I think when you talk about the Mirror Universe, I know a lot of people think it’s overdone, but I’m like you, I love it. And there’s a reason that it’s only in for like eight minutes of the episode, but who didn’t want to see that? Come on. And so, we thought that at least some of the Mirror Universe might say, ‘Let’s return to our old ways and form the new Terran Armada.’ And that’s where we get to Mirror Janeway, which was loosely inspired in some aspects by the Mirror Janeway we see in Star Trek Online, but we added our own touches too.

On the cutting room floor, I think we also had like maybe one more level on that “Cracked Mirror” episode. That was an episode where the Borg won because that felt like a fun Janeway thing. And I think we saw a little bit of that universe in “Parallels” with the famous Riker thing, where he’s commanding the damaged Enterprise when they have all these Enterprises coming from different universes. And he’s like, ‘I’m not going back. I can’t go back.’ And then he explodes. I think that’s haunted Trekkies’ dreams for so long that we wanted to see, ‘Well, what would Janeway be doing in that universe?’ And in that universe, they had all been assimilated, and Voyager had become like a Borg ship. And so they had to get through that universe to alongside the Mirror Janeway to try to undo this mess. But you know, if it was a 44 minute episode, oh, the tails we could have woven.

Time Travel & Temporal Mechanics 101 In Star Trek: Prodigy Season 2

Let’s talk a little bit about time travel. I did not read Temporal Mechanics 101. So I did not fully grasp all the time travel and time paradox stuff that was going on, but I went with it. It sounded like it made sense.

Aaron J. Waltke: Well, I could give a full hour TED talk actually laying out everything, but I will try my best. You know, we talked about it being a time loop. And in a sense it is, but in some ways, it’s more like a time figure eight. Star Trek has said in multiple series, “Parallels,” especially Enterprise with the Temporal Cold Wars, with different timelines invading the Prime Universe and whatnot, that there are parallel realities, and all timelines exist independently. But I think what throws people for a loop is we’re following the Prime Timeline. That’s the one we care about. And Star Trek has shown that that timeline can get messed up, and then they have to set it right. But that doesn’t preclude the other timelines from existing. And so, we made it very clear at the end of season one that Chakotay was trapped in, and the Diviner came from, an alternate future timeline. So, a timeline and parallel to ours were where Solum was destroyed. And when the Diviner came into the Prime Universe, he was effectively like, ‘My Solum is lost, I want to create a solum here, that survives. And in theory, it will survive, it will thrive.’

And so, we get a little hint of that in season two, in Asencia’s final monologue. She says,’The multiverse holds a bitter truth, girl, that my Solum will always be lost.’ Which is true. And so she’s bent on vengeance, and she wants to sort of shape this reality like a blank slate into whatever she wants. But that means that you now have two universes that can kind of interact with each other, and Gwyn’s past lies in the events that happen in that alternate universe. Because if the diviner didn’t come to Tars Lamora, then he’d have no reason to mine it. And then he’d have no reason to eventually get sick and create Gwyn. Which is what I think Janeway says very clearly, like, ‘She’s the only one in this universe whose existence depends on the Protostar being there,’ which is why she starts fading in and out of existence.

Some people have said, ‘Well, how come one thing causes a paradox and one doesn’t?’ Well, as you’ve seen in Star Trek, Picard, and in our show, and even in TNG when Wesley first meets the Traveler, you know, he’s like, ‘There are things beyond your comprehension.’ I think Picard even says like, ‘Are you from the future? Are you from a different universe?’ And the Traveler says, ‘Yes, according to how you would understand it.’ So basically, he makes it very clear that there are calculations of play that even with 24th century technology, we don’t fully understand which moments in time can be altered and which ones can’t, safely.

The Difference Between Star Trek: TNG’s Nova Squadron & DS9’s Red Squad

Let’s talk about something a little simpler: Nova Squadron. I was genuinely surprised that Nova Squadron is even still a thing after TNG, and then Red Squad in DS9. But I’m always suspicious of elite cadets. Elite cadets to me are bad news. Let’s clarify: Maj’el and her friends – Are they in Nova Squadron or are they hopefuls like Dal and his friends? Because they had the pins.

Aaron J. Waltke: So this is something that has kind of been alluded to in TNG, especially in “The First Duty,” and you see a little bit of it in Lower Decks. And then also, there’s Deep Space Nine episodes like “Valiant” that deal with [Starfleet Academy] squads and that sort of thing. And I think the way that we viewed it was we likened it to be a little bit like Top Gun. Like, there’s a little bit of a rivalry initially, between Iceman and Maverick. And you hate Iceman. But then, as the show goes on, you’re like, ‘Oh, they’re just pushing each other to be better.’ And in the end of Top Gun, Iceman comes around, and they help each other because ultimately, even though there’s a friendly rivalry, they’re all part of the same organization trying to make the world a better place. And that’s how we wrapped our heads around how you can have that kind of competitiveness in the utopian society.

In terms of Maj’el, and Grom, and Zeph’s place in [Nova Squadron], in the opening, you hear them referred to as Nova Squadron candidates. So I don’t think this has ever been elucidated fully in Star Trek lore, but we kind of visualize them as a little bit like fraternities with specialized training. Nova Squadron tends to be more about sort of helping conn officers become their best selves, whereas Red Squad, I think, is more specifically about command or something to that effect. So in this case, they’re candidates, so we viewed them a little bit as like pledges in a probationary period to join Nova Squadron. They want to prove themselves on this mission with Voyager in order to get fully accepted into it. And you’re right, they do have the pips, the Academy pips, which means that they are, in fact, in Starfleet Academy, which kind of further solidifies in some ways that rivalry [with the Protostar kids]. They went the traditional route, they spent years training, got into the Academy, and I think Maj’el even has four pips. So she’s pretty well along and is excelling. And then here come Janeway’s troublemakers who have hardly any experience beyond a little bit of prep training. And now they get to be on the ship and are sort of treated as teacher’s pets.

And so, you understand there’s a little bit of ‘How did they get in there?’ And I think we even had a scene that unfortunately was cut for time in the pilot, where they are playing Parrises squares against each other, and Nova Squadron just dominates, And then [Dal’s friends are] like,’You’re being unfair’. And Maj’el says, ‘You are correct. This is unfair. Why did you get to jump to the front of the line when there are clearly far more qualified candidates to be on this mission?’ So it all comes from a place of logic wrapped up with the pressure to perform, and ego. But ultimately, as you see, as the season goes on, they kind of come together, and Dal gets to sub in for Grom in Nova Squadron. And they’re like, ‘we all have something to teach each other.’ And that was where we wanted to go with that.

Captain Chakotay’s Purpose In Star Trek: Prodigy Season 2

I also cannot say enough great things about how awesome Robert Beltran’s performance was. He was absolutely fantastic as Chakotay. And it seemed like it was a combined effort with the writers and also with Beltran to put on the best Chakotay we’ve ever seen on screen.

Aaron J. Waltke: Yeah, I think there’s no question that the character of Chakotay was not used to his full potential previously. And there were certain aspects of his character, especially his heritage, where we listened to the indigenous community who said, ‘We don’t want him to be just from a made-up tribe, we want a heritage that is actually real and would align with what we know about his backstory, and where Robert himself has his lineage from. And so, it was important to us to try to rectify some of those mistakes.

It was very important for us to give Chakotay a meaningful presence in our show. I think one thing that Prodigy’s philosophy has always adhered to is if we’re going to bring in a character, we don’t want just someone that our main young crew is inspired by, but they themselves have a story. And that they are, in fact, affected by the storyline of Prodigy themselves. And so, we knew we had our work cut out for us, but we also had the elements of Chakotay’s character that we loved. He’s someone who is bound by duty, honor, and loyalty above all else. And sometimes you can get lost in that. And I think even the character of Chakotay got lost in that when he first joined the Maquis. But in doing so, he became a great reflection of where Dal was when he kind of felt out of place. And he helps Dal realize that you don’t have to be captain in order to be worthwhile. You just have to find where you belong. And that’s what that whole mentorship really reflects.

Aligning Wil Wheaton’s Comeback As Traveler Wesley Crusher With Star Trek: Picard

Wil Wheaton as Wesley Crusher is a total home run. When I spoke to Kevin and Dan, they gave me a little background on Picard and Prodigy and how you guys coordinated Wesley in Picard season 2, but how did that all shake out? A little bit more detail on that?

Aaron J. Waltke: Sure. We had written the season overview and had broken almost all of the episodes of season two. What we were doing with Wesley Crusher was baked into our season pitch to the network. We want to bring back the original prodigy to guide them through this sort of temporal Gordian knot they find themselves in. So when Picard season two came along, and they were interested in exploring similar themes, obviously, we made sure first that our shows didn’t overlap. They were both two seasons dealing with timey-wimey stuff. And then in terms of bringing in Wesley, specifically, as [Picard’s] final episodes came in, they reached out to us and they were like, ‘Look, we’ve alluded to the fact that we’re going to have time travel. We have supervisors in our season. And we’ve alluded to the fact that they’re tied to the Travelers. We would like them to meet a Traveler. And, it could be a random person, but we know what you’re doing with Prodigy. Is there a way that it could be Wesley?’

We got on several calls with Akiva [Goldsman] and then eventually with Terry [Matalas] as we dealt with the second half of the season. Just plotting out: Okay, what is Wesley’s role in this organization? Is he sort of middle management? Is he in charge of it? Or was he somebody who was left behind? That’s last one is the one that we kind of went with, in that he was an up and comerr. Probably, if he kept going, he might eventually become in charge of it. But instead, he’s the one who stayed behind at the lighthouse trying his best to make sure the ships come in to sea. We wound up having a lot of deep-dive conversations about the organizational structure of [the Travelers and] Wesley’s place in it. But also, when it came down to the monologue that he had [in Picard], Akiva was generous enough to send us the scene and said, ‘Does this work? Please do whatever you need to it.’

I was able to rewrite a little bit of it to conform to everything that we’ve already talked about. And he let us slip in a couple of deep allusions to Prodigy itself, when Wesley says, ‘A star Is born, but a ship is lost. A new species thrives – the Loom – but a civilization collapses – Solum.’ We were hoping, and fans, thankfully, are starting to make that connection, that it was all part of the same thing, of Wesley’s journey across these two shows. And then obviously, with the return of Jack [Crusher], we knew that Jack was a character in Picard. But it also opened up the question of, ‘Well, we obviously are using Beverly Crusher in our season as sort of an anchor for Wesley. So if he’s going to visit and reconnect with his family, it should be his whole family. Because Jack would be a few years old at this point. Interestingly, we didn’t have the budget to build a Jack rig. So we were like, ‘Well, can we get away with staying on Wesley’s face and hearing the voice of his little brother.?’ And I think that actually became far more poetic and moving. And thankfully, the fans agree.

I think it was amazing that the Wesley and Beverly reunion happened on Prodigy and not Picard, where we were all expecting it. It was still totally satisfying. It doesn’t preclude a live-action reunion in the future and Wesley and Jack meeting as adults. But it was really nice in this time period to see Wesley and Beverly interacting finally.

Aaron J. Waltke: Terry was very generous, and even Wil and Gates both weighed in. We all basically formed a brain trust of, ‘Let’s make sure this feels right.’ And we agreed that even with where Beverly is in Picard season three, 15 years may not be much to a Traveler, but it’s a lot to a human. So that meeting we see is a little bit bittersweet, and he may not show up in between then and Picard season three. But you’re right, it doesn’t preclude them reuniting thereafter.

Star Trek: Prodigy Season 2’s Ending Tying Into Star Trek: Picard Season 1

Let’s get into the ending. The Picard tie-ins to the finale. “Children of Men” is my favorite Short Trek. So tying that into Prodigy made me so happy. I wrote an article recently about how the Mars attack was worse than we knew. Prodigy clarified some stuff about how crippled Starfleet really was. So let’s talk a little bit about the details of that. The A500s turning and Utopia Planitia being destroyed. There’s a lot of intricate stuff involved that Picard touched on, but now Prodigy has delved into a little bit more.

Aaron J. Waltke: You’re right, We saw 2385 in Picard, and they had maybe like five minutes total, all in flashbacks. Obviously, Starfleet and the universe is a very big place. And we wanted to expand on why. Why and how did this deeply affect Starfleet? Even beyond just the rescue mission for the Romulan evacuation? And we realized that the 2380s is relative peacetime. So Starfleet is expanding rapidly, especially in the wake of the Dominion War and with the Shinzon Incident behind them. They’re like, alright, it’s clear skies. It’s blue skies. Let’s go push ourselves as far out as we can on the horizon, but they wound up overextending themselves. And so, for a lack of engineers, they brought in the A500 units to start filling that gap. And I think there’s a line from Jellico where he says, ‘A500s are barely keeping member worlds going’, implying that they’re not just used at Utopia Planitia, but they’re used across the Federation to fill that lack of manpower that you need with engineers.

So when you take that out, suddenly, imagine any organization suddenly loses 30% of what it needs. It’s going to be devastating. And you do start to understand why they would be like, All ight, we have to claw back and reassess. But, as we’ve seen with Janeway, not everybody agrees with that sentiment, and the spirit of Star Trek is exploration. No organization is a monolith. And there’s going to be debate, as we’ve seen in plenty of ready rooms. And we thought, wouldn’t it be interesting if Janeway, after being called out of retirement, cashes in all of her chips and says, ‘Just from a purely philosophical perspective, we need to have someone out there that can be on a goodwill mission. Of course, we have seen multiple goodwill missions from across Star Trek that are manned by cadets. I think even Nog says in Deep Space Nine, ‘I’ve heard of plenty of runabouts being commanded entirely by cadets.’ Even in the TOS unaired pilot, one of the first things that Pike says is, ‘What are we running here? A cadet ship?’ So clearly there are cadet ships out there, but ours is the first show to really focus on them, hopefully, in stories to come.

So we know what the USS Prodigy’s mission is in season 3, should that happen. Knock wood it will. But Chakotay is now Captain of Voyager-A. So what is their mission?

Aaron J. Waltke: Obviously, we’ve made it clear that the Federation’s pulled back their borders, but that doesn’t mean there’s not still problems within the Federation’s borders that need fixing. So I think, like the Enterprise was used as a Swiss Army Knife sometimes elsewhere, not [fighting in] in the Dominion War [because] there were other fires to put out, in my mind, the Voyager-A has a similar mission where even within the confines of where they’re allowed to operate, there’s plenty to do as always.

Well, it’s funny because the Protostar’s original mission was to right whatever wrongs of the original Voyager in the Delta Quadrant, and that didn’t actually get accomplished because they fell in a wormhole and then ended up in the future. Potentially, Chakotay could do the job he originally wanted to do five years prior.

Aaron J. Waltke: Very possibly. Yes. Interesting. And while we’re talking about the ending, I just wanted to say that one of my favorite Easter eggs that we threw into Janeway’s Admiral’s log was a very deep-cut allusion to the DVD extras of Nemesis, [which] has a deleted scene in which you hear Picard and Data sort of ruminating on the nature of time. It was such a beautiful scene, and I was like, ‘It’s too bad that’s not canon.’ And so, when you hear Janeway, who we’ve seen at the beginning of Nemesis is like, ‘Hello, Jean-Luc,’ so they’re clearly have become friends, she says, ‘An old friend once told me that we’re not affected by the passage of time, but the presence of time within us.’ She’s, in fact, alluding to something that Picard has supposedly told her. But go back and watch the scene. It’s a beautiful scene.

About Star Trek: Prodigy Season 2

In Star Trek: Prodigy Season 2, the six young outcasts who make up the Prodigy crew are assigned a new mission aboard the USS Voyager-A to rescue Captain Chakotay (voiced by Robert Beltran) and bring peace to Gwyn’s (voiced by Ella Purnell) home world. However, when their plan goes astray, it creates a time paradox that jeopardizes both their future and past.

Check out our other Star Trek: Prodigy season 2 interviews:

Star Trek: Prodigy

Writers

Dan Hageman , Kevin Hageman

Showrunner

Dan Hageman , Kevin Hageman

Franchise

Star Trek

Creator(s)

Kevin Hageman , Dan Hageman

Number of Episodes

40

Expand