Warning: This interview contains spoilers for the season 2 finale of Star Trek: Lower Decks!

With Star Trek: Lower Decks season 2's finale, the animated comedy series upped the ante by dropping a shocking Star Trek: The Next Generation-style cliffhanger: Captain Carol Freeman (Dawnn Lewis) is arrested by Starfleet Security and accused of blowing up Pakled Planet. This leaves her daughter, Ensign Beckett Mariner (Tawny Newsome), and the crew of the USS Cerritos wondering what will happen to the ship and their beloved Captain.

Screen Rant spoke with Star Trek: Lower Decks creator and showrunner Mike McMahan about season 2's cliffhanger, the rise of Ensign Brad Boimler (Jack Quaid), and the long-awaited debut of Cetacean Ops. Plus, McMahan dropped some fascinating clues about what's coming next in Star Trek: Lower Decks season 3.

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Screen Rant: Mike, what a great finale to a fantastic season 2. I loved the TNG-style cliffhanger at the end. 

Mike McMahan: Right?! Getting to do that with the TNG font on the screen and Chris Westlake's score, I was like... [triumphant laugh].

Let's talk about that cliffhanger. I’m gonna go out on a limb and guess that Captain Freeman didn’t destroy Pakled Planet?

Mike McMahan: Well, listen man, there's a whole lot in this galaxy that would blow your mind. And Captain Freeman, she is known for wanting to make a big splash. But it does seem *a little* out of character. [laughs] So, I wouldn't be surprised if you're right.

Looking back at the last two episodes, I’m definitely seeing a pattern where episodes 9 and 10 of the season are just the greatest. “Crisis Point” and “No Small Parts” in season 1 and this year, “Three Ships” and “First First Contact”. You really know how to ramp things up to end a season.

Mike McMahan: Thank you. What happens is we're doing all these episodes, we're doing all this character work, we're trying to do all this stuff, and my number one goal for the penultimate and ultimate episodes are: Let's do something that breaks form and is a little more cinematic for the second-to-last episode. That's how you get the movie episode ["Crisis Point"], that's how you get "Three Ships," which is my pitch to Paramount: let me make that into a movie! And then for the finales, I'm always like, "What feels like a finale? What wraps everything up? What introduces new ideas? And what leaves the audience saying, 'Holy crap! I love this show!'"

From your tone, I hope we hit that because I really love this finale. I mean, getting Cetacean Ops in there alone was my dream! I got to do it. I've been waiting my whole life to do that.

And I never would've guessed how horny dolphins are for swimming with humans.

Mike McMahan: They are so horny in real life! I'm just going off of real cetaceans. And those aren't dolphins, they're Beluga whales. Also horny. Mammals are horny. That's our whole thing.

You know what, that's probably Gene Roddenberry's other message.

Mike McMahan: Yes, his other vision. Hey listen, infinite combinations, right?

In episode 9, which was amazing, you also introduced new Lower Deckers on other ships. Will we see T’Lyn (Gabrielle Ruiz) again in season 3?

Mike McMahan: You will see T'Lyn again, but her story does not take her to the Cerritos any time soon.

Season 2 very much felt like Boimler’s time to shine. He never stopped being the Boimler we love but he kept rising to the occasion and saving the day. 

Mike McMahan: Thank you. We love all of our Lower Deckers and our goal for each season is to feel like we're moving them forward. I've often said Lower Decks is more about personal discovery rather than space exploration. You know, at the beginning of the season, you've got classic Boimler but when he gets split [into Brad and William Boimler] and [Brad] comes back to the Cerritos, that's the first moment where it's like, "Wait a minute, I've grown a little bit."

I think Boimler always had it in him and I think Mariner always saw it, but once he started getting this confidence and once he started being a little less of a person who is playing the game of Starfleet and just [began] doing the right thing and being in Starfleet, Boimler's a guy you can really get behind. Mariner's always known that about him, that's why she wanted in the pilot episode for her and him to be cha'DIch.

And what a great moment at the end of episode 9 when the other Lower Decker comes up to him and asks him to be his mentor.

Mike McMahan: The cadet. Yeah, I really love that moment. And you see [Commander] Ransom glance at them. Ransom's a good guy at heart. Even if he did lie about being from Hawaii, which is not cool.

Well, apparently, everyone in Starfleet lies about being from Hawaii, so...

Mike McMahan: You either lie about being from Hawaii or you talk about Riker being from Alaska. It's always one of those two things.

I also really like the slow burn story you’re telling about Rutherford’s that has been going on since season 1. Will Rutherford learn why he got the implant in season 3?

Mike McMahan: There's an episode in season 3 that answers a lot of questions about the implant. A lot of things that Rutherford thought he knew that weren't right. There's a lot of stuff that ties together. Like, you see the implant malfunctioning a lot in the first and second season. There's something about the implant that hasn't been discovered yet.

And remember, this is Rutherford's second implant. He lost his first one at the end of the first season. So it's not only part of the implant story but it's about Rutherford himself and why he needed the implant. Because nobody else has those. There's a reason [Rutherford has it.] It's a little of my Julian Bashir, kind of, backstory. Not one-for-one but that's kinda what got me excited [about Rutherford's backstory].

Speaking of Deep Space Nine, when Dr. T'Ana told Tendi she didn't know who Jadzia Dax was, you kinda stabbed me in the heart.

Mike McMahan: [laughs] Well, the funny thing is, of all the times everybody knows everybody, of course, somebody has to not know at one point and it's gonna be Dr. T'Ana. That's so funny.

I mean, it makes sense. Of course, everybody knows who Spock is. I get it.

Mike McMahan: Yeah, it's like, Tendi is us and Dr. T'Ana is probably our parents, you know what I mean? They're still Trekkies, they just don't know who Tilly [Mary Wiseman] is, you know what I mean?

To quote you, season 2 ends with some bills to pay for season 3. The Cerritos has to be rebuilt again. That was amazing, stripping the ship of its hull plating.

Mike McMahan: That's based on one of my favorite [Star Trek:] Enterprise episodes, which is the "Minefield" episode, where debris gets stuck on the hull plating. But doing it to the whole ship, I was like, "Nobody's ever done our girl [the Cerritos] that wrong before on a Star Trek." In the movies, they crash 'em but nobody's ever had to strip the ship.

When season 3 kicks off, I’m guessing the Cerritos will have a new Captain, at least for a while. Which seems like Mariner’s worst nightmare. What's next for her?

Mike McMahan: The next thing that you'll be seeing that we're addressing in season 3, and I'm gonna be careful how I say this, is: How does Mariner handle not only her mom no longer being the Captain of the Cerritos but bring untrusted by Starfleet, [put] on trial, and being taken away from Mariner. Mariner's always being told, "You're lucky I'm not kicking you off the ship." But what happens when your mom has been kicked off the ship by Starfleet? That's all I really want to say about that.

Well, thank you for talking to me. It'll be a long year or however long it is until season 3.

Mike McMahan: Thank you so much. All of season 3 is written. We've been seeing animatics. It continues to be a blast. I cannot wait for you guys to see it.

Next: Star Trek: Lower Decks Season 2 Ending & TNG Connection Explained