Captain Janeway’s return to Star Trek feels long overdue.

The last time fans saw Kate Mulgrew’s iconic commander of the starship Voyager was on the big screen, in a short but exciting cameo in 2003’s Star Trek: Nemesis. Now, she is back in animated form with a vital role in Star Trek: Prodigy, Paramount + and Nickelodeon’s new animated series. The first Trek aimed at kids, Prodigy — created by Dan and Kevin Hagman — finds a group of alien teens trying to evade sinister forces in the Delta Quadrant with the help of their shiny new (and recently unearthed) starship and a holographic version of Janeway. Tonally, Prodigy is Star Trek by way of The Goonies. So it makes sense that fans’ bridge to this new show is a character who has a history with helping found families find themselves among and across the Final Frontier.

With seven seasons of Voyager and more than 25 years with the franchise under her belt, it would be easy for all of that “boldly going” to blur together for the actor. But for Mulgrew, there’s one voyage that really stands out, her favorite episode of Voyager: Season 5’s “Counterpoint.”

“That’s my favorite. And nobody ever, ever [talks about] it!” Mulgrew told SYFY WIRE at a recent NYCC event for Prodigy. The episode is an underrated gem for the series, but a fan-favorite thanks to its rich character work and keep-the-plates-spinning tension.

“It was originally pitched, I believe, to us, as The Diary of Anne Frank on a starship,” Mulgrew recalled. Writer Michael Taylor mined that dramatically exciting premise with a riveting episode where Janeway struggles to smuggle telepathic refugees through a region of space where telepaths are illegal. The farther she takes them through this dangerous stretch of the galaxy, the harder it gets for the captain to outwit (and not fall for) the charming and cunning alien in pursuit, Kashyk (played by Mark Harelik). For the first time in the series’ history, Janeway is given a very compelling and complicated love interest — her enemy — which is in part why the episode has stuck with Mulgrew since it aired 23 years ago.

“It’s the first time we have seen Janeway perplexed in a deeply emotional way,” Mulgrew explained. “Is she really falling in love with him? Is he seriously in love with her? Or is it just a ruse? What a rich, wonderful story to play with,” she said. “No one really talks about this episode. They always bring up ‘Year of Hell’ or one of the Borgs, but this one… there are so many layers, and all of those nuances — the subtext — was so great to play.”

Also great for Mulgrew was her scene partner.

“Mark was terrific in the role. I loved it. I thought the acting was excellent, as far as performances go. This was the type of love story, or complicated romance, that I so, so wanted to play and explore with the character. It was five years in at that point, and we just — aren’t you great for wanting to talk about it!” [Editor’s note: As a lifelong Star Trek fan, there is life before and life after Captain Janeway calling you “great.”]

When it comes to singling out a favorite scene or experience from the making of the episode, that is tricky for Mulgrew.

“I loved it all. That entire episode is very, very vivid in my memory. Because I was matched against a great actor, in a story that I loved. She was so lonely, lost in the Delta Quadrant for a long time. Every thing in her, up to that point, had been tapped. And finally, it’s possible that she can be a woman. But, sadly, it proves to be not possible. I ran to work each day to shoot this. I was very sad when it ended.”

Mulgrew, like her character, was also very tapped out as an actor by the time the episode wrapped.

“How does your heart break without showing physical representation? Because Janeway must conceal this. So it was very, very challenging work and I really loved that.”

Not challenging for the actor was bringing her most famous role back to the small screen. Especially when facing the unique needs of an animated series.

“I think a recording booth is my heaven. It’s a pleasure, a real pleasure. It’s just me, my headset, the mic, [the showrunners] on Zoom, and the [audio] engineer though the glass, and it all gave me this wonderful sense of: It’s mine. It is also very liberating.”

With the liberation that came from not being bound to standing sets on a soundstage, or to the rigors of an early call time for makeup and wardrobe, Prodigy also afforded Mulgrew an opportunity to find a new way into her very familiar character.

“It allowed me to develop new methods,” Mulgrew shared. “New nuances and subtlety. New methods of vocal control. These are sort of hard things to learn, so I used this [show] as an opportunity to take on those challenges and deepen those skills.”

But the actor is very mindful that she wouldn’t be able to reconnect with Janeway if it wasn’t for episodes like “Counterpoint”.

“You have to understand, this was almost a decade of my life. A decade that never really ended, as you can see. And now, to come to a kind of full circle with it — and after talking about ‘Counterpoint’, all the memories are coming back — I am delighted to be here, with her, once again.”

Star Trek: Prodigy premieres Oct. 28 on both Paramount+ and Nickelodeon.