This article contains spoilers for "Star Trek: Lower Decks" season 3, episode five.

"Star Trek: Lower Decks" has done something that almost seems impossible, mixing an animated workplace comedy with the most important themes and lessons of the "Star Trek" franchise. While the series approaches many things with the flippant attitude necessary for a comedy, it also handles the Starfleet of it all with a lot of love and nuance. Series creator Mike McMahan has said that the ultimate goal is to create episodes that feel like real "Star Trek" while also being funny. In order to do that, the series might have to occasionally get a little dark. Okay, a lot dark, like having the ship's sweetest goofball find out that his cybernetic implants weren't elective to help with engineering, but were actually a part of an elaborate cover-up after an accident. Fans got a taste of Ensign Rutherford's (Eugene Cordero) past at the end of season 2, but in season 3's "Reflections," we learn a whole lot more.

Over the course of two and a half seasons, "Star Trek: Lower Decks" has had a few ongoing story arcs that play out in pieces while still serving the sitcom-style A-and-B plots, but "Reflections" hints at a future that's slightly more serialized. There's still going to be plenty of wacky hijinks, as shown by this week's other storyline following Mariner (Tawny Newsome) and Boimler (Jack Quaid) at a job fair, but there might be some detours into disturbing territory.

Repressed Memories Are Rough

The happy-go-lucky Rutherford has some blank spots in his memories, but they usually don't seem to bother him too much. In "Reflections," however, he keeps having a recurring nightmare about some kind of accident and it's keeping him from getting any rest. A concerned Tendi (Noël Wells) does a scan on him and notices some long term memories stuck in his implant's cache. She clears the cache for him, hoping that will improve his quality of sleep, but instead it breaks down the barriers in his mind enough for a different version of himself to take over. This version of Rutherford isn't exactly okey-dokey — he's angry and wants to steal the Captain's yacht. It turns out that this Rutherford is the one that existed before the implant, and before the accident that current Rutherford keeps dreaming about. "Evil" Rutherford is actually just a younger version of himself, with all of his memories intact, and he wants control permanently.

Shax (Fred Tatasciore) knows that Rutherford isn't "himself" and manages to stop him from escaping the Cerritos and gets him to sick bay. While in a coma, young Rutherford and older Rutherford agree to have a race through space in order to figure out who gets to keep control of their body, since both can't exist without overwhelming their brain. Young Rutherford was into illegal space races, which baffles the Rutherford we know and love, and it looks like the younger version might win the race. Thankfully, elder Ruthy manages to bring imaginary versions of his friends into his mindspace to help, and they win in the end. Though the younger version begins to fade, he does share one last bit of wisdom: the events surrounding Rutherford's accident and implant.

A Starfleet Cover-Up

Apparently, Rutherford was involved in some kind of engineering testing program and had an accident that caused some serious injuries. While being operated on, he witnessed someone in a Starfleet uniform telling the doctors how to cover things up. They would program memories of the implant being an elective choice, and they would wipe everything having to do with the program and the people in it. Nearly a decade of memories were erased, by someone in Starfleet, to cover up something they weren't supposed to be doing.

"Star Trek: Lower Decks" has reassured fans that Starfleet is a force for good, generally, by showing their capability in the season 3 premiere. Instead of just accepting the word of the Pakleds, Starfleet intelligence arranged a covert operation to dig into the truth of things. Starfleet were the good guys, they kept Captain Freeman out of prison, and everything was hunky dory. Unfortunately, life isn't as neat and clean as all of that, and there is a darker side to Starfleet, too. Not only can individuals within the organization get up to nefarious deeds, but the shady Section 31 are notorious for techniques that the Cardassian military might even find immoral. Rutherford is the most innocent, sweet character on the Cerritos, and giving him such a potentially dark past hints at where the series might go. It also makes him significantly more complex, which is a big part of what makes "Lower Decks" so great. These characters are better fleshed out than some of their flesh-and-blood counterparts on live-action "Trek" shows, so the stakes feel exceptionally high.

The Beautiful Duality Of Star Trek: Lower Decks

The first two seasons of "Star Trek: Lower Decks" showed fans that "Star Trek" could be really funny, and season 3 is showing fans that an animated comedy can evoke just as much feeling as any of the live-action shows. "Lower Decks" is still "Star Trek," and the franchise has always been willing to dive into some seriously uncomfortable territory. "Reflections" is great because it shows the duality of "Lower Decks" so well. Boimler and Mariner get to wreak havoc and create comedy, while Rutherford has a truly engaging sci-fi side plot. That's "Star Trek," baby. Here's hoping they can maintain this balance for many years to come.

New episodes of "Star Trek: Lower Decks" debut Thursdays on Paramount+.

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