‘Star Trek: Lower Decks’ Theory: The Mysterious Season 4 Threat May Not Be What It Seems

Mystery ship fires the beam weapon in "Twovix"

The latest season of Star Trek: Lower Decks has kicked off with a bang, introducing a mysterious new threat to the galaxy. This threat is part of a season-long arc that will likely be wrapped up in the 10th and final episode of season 4, but we don’t have to wait that long to indulge in some informed speculation. The following theory article includes spoilers for the first two episodes along with possible spoilers if we are right. [EDITORS NOTE: The author of this article has not seen any episodes beyond episode 2]

Lower Decks introduces a new mystery

In the first two episodes, an unknown vessel has destroyed a Klingon ship and a Romulan ship. The attacks appear to leave no survivors. This ship, a design never before seen in the Star Trek canon, has become the focal point of fan discussions, especially after its dramatic appearances in the first two episodes of the season.

At the end of the premiere episode, “Twovix,” this mysterious ship barrels into Klingon space and annihilates a Bird of Prey. In episode two, it takes down a Romulan Warbird after seeing through its cloak. But what if there’s more to this ship’s actions than meets the eye?

Romulan warbird encounters the mystery ship in “I Have No Bones Yet I Must Flee”

The Unknown Vessel: What We Know

Before diving into the theory, let’s recap what we know about this enigmatic ship…

  • Unique Design: The vessel boasts a design never before seen in the Star Trek universe. This raises questions about its origins. Is it from a previously unexplored region of space? Or perhaps a creation of a known species, developed in secret?
  • Solo Operation: When the Klingons scanned it, they said the ship contained one life form. This suggests a level of technological advancement where one being can control such a powerful vessel.
  • System Disabler: Much like the “whale” probe in Star Trek IV, the unknown vessel has the capability to disable other ships’ systems, rendering them vulnerable.
  • Romulan Cloak Detector: In episode 2 the vessel was able to see through the Romulan cloaking device, a feat that few ships in the Star Trek universe have achieved.
  • Unprecedented Power: The ship’s firepower and capabilities are off the charts, making it a formidable adversary for any fleet.

Mystery ship fires the beam weapon at Klingons in “Twovix”

The Transport Theory

The crux of the fan theory is that the unknown vessel’s victims weren’t actually killed but transported elsewhere. There is precedent for using transporters as weapons in this way (TNG’s “Gambit,” and the film Insurrection to name a few). Most recently in Picard season 3, we saw Raffi and Seven shoot the Borgified bridge crew with a phaser rifle, transporting them to the brig. Perhaps this vessel has harnessed a new form of transportation, one that can move entire crews instantaneously to a different location. It might also be worth noting how the main story for the premier episode was about the dangers of the transporter and a transporter being used for evil purposes, in this case, “T’Illups” using it to “Tuvix” members of the Cerritos crew.

There may be a clue backing up this theory in the official synopsis for season 4 which reads in part “… an unknown force is destroying starships and threatening galactic peace.” While “destroying starships” may include the killing of the crews, it is not necessarily true they are being killed. Notably in neither the Klingon nor Romulan attacks were any bodies spotted, just debris from the destroyed ships.

Debris of the Romulan from “I Have No Bones Yet I Must Flee”

Also, a new threat killing off hundreds or thousands of aliens for no reason is pretty dark for this comedy series. This includes the previously known (and liked) characters in the crew of the IKS Che’Ta’, the Klingon ship introduced in the fan-favorite episode “wej Duj.” Episode 1 included revisiting some of the characters from that episode, making their apparent murder all the more surprising. While kidnapping the crews and destroying these ships is still immoral behavior, it’s not mass murder, which is a bit of a comedy buzzkill for when this all gets wrapped up later in the season.

Captain Ma’ah of the IKS Che’Ta under attack from the mystery ship in “Twovix”

The Destination: Where Are They Going?

But why transport and not kill? The motive remains unclear. It could be an attempt to gather intelligence or even to recruit from various species for a yet-unknown purpose. The destroyed ships might serve as a diversion, a way to instill fear and prevent any pursuit or investigation into the true nature of the disappearances. We have seen plenty of Star Trek adversaries holding prisoners, including those presumed to be dead, especially during the Dominion War.

If the theory holds, the next big question is: where are the victims being transported to? A hidden planet or space station? Another dimension or time? The possibilities are endless, and each brings its own set of intriguing narratives.

One possibility is that the unknown vessel’s pilot is collecting species for one of the other top thousand menageries in the quadrant, now that Narj is out of the picture. Alternatively, the victims could be transported to a paradise-like realm, where they live in peace, unaware of their past lives. Or perhaps they’re being taken to a battleground, forced to fight for the entertainment of a powerful entity.

Narj’s Miraculous Menagerarium from “I Have No Bones Yet I Must Flee”

There are always…possibilities

Of course, these are just some of the possible explanations for the unknown vessel’s actions and intentions. There are other theories out there and I’m sure more will be revealed in future episodes. Either way, the Cerritos crew will eventually get on the case, and they will no doubt stop at nothing to uncover the truth behind this enigmatic ship and its true intentions. In the meantime, fans can continue to speculate and theorize about this mysterious new threat. It’s sure to be a hot topic of discussion for the rest of the season, especially as we learn more about the mystery threat, possibly as soon as episode 3 debuting on Thursday, September 14.

We already have a few thoughts on some possible suspects for who is behind the mysterious new threat so stay tuned for more theories on Lower Decks season 4 here at TrekMovie.com.

What are your thoughts on this theory? Do you have theories of your own about the mysterious new threat? sound off in the comments below.

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The ship looks like the Agonizer from the TOS episode “Mirror, Mirror.” Does no one else see that? Right?

To me it looks like a cross between a buffalo chip and the Orville’s shuttlecraft.

Kinda getting Boba Fett ship vibes.


My bet is S31 and William Boimler are involved. It might be too obvious.

First think it makes me think of is the Romulan holo ship from Enterprise season 4

I hope the transporter theory is true. It’s better than what I thought which is that all of their bodies had been disintegrated.

Joke theory: it’s the Wadi and all of the people on the targeted ships are trapped in the game.

I really like the transporter theory and seen others online and YouTube suggest the same thing. I really don’t want the Klingons to die, I wanted to see more of them after Wej Duj. But it’s a good mystery so far.

We’re ending the season with Cerritos-A, aren’t we? I just know that this really weird love letter to support vessels will end up with Mariner saving the day but the ship getting blowed up real good.

Just since nobody has mentioned Shatner thus far, I’m gonna say mirror Kirk is behind this.

I think section 31 makes sense. They probably studied the whale probe from The Voyage Home. Which brings that Easter egg to another level in the opening credits. Did anyone else think the movement of the vessel is similar to Spock’s vessel in the Star Trek reboot?

First thing I thought was it looks like a Shuttlepod from Enterprise.

I was thinking its S31 Boimler and Badgey have made an alliance

Guessing the mystery ship has something to do with the whale probe since the probe has been added to the opening credits and it also caused ships to lose power.

Eh, pretty sure the whale probe is just there cause STIV/STLDS4.

The Voyage Home tie-in to Season 4 makes it more likely to be the whale probe, not less.

mirror universe episode is coming up ,…..looks like an agonizer ship

I see an evolution of Gomtuu

The vessel and its occupant could be from the future.

I think the mystery ship looks kinda like Pike’s chair (as seen in this version of Pike), and that this is the result of the events of the crossover episode with Strange New Worlds.

I was wondering if they were doing a V’ger digitizing thing for a minute, but they have shown wreckage afterwards so I’m guessing the ships are actually getting destroyed.

The shatner idea is interesting since he’s never appeared out side any tos and fans are screaming for it. It seems the ship is going after one of each of our aliens, are the talosians up to their old trucks? Maybe a pike crossover? He’s out body hunting for talosians.