Star Trek: Deep Space Nine/WMG

Everything About Fiction You Never Wanted to Know.


Bashir's genetic enhancements were done on the order of Section 31

Bashir's parents were constantly changing jobs, so it is unlikely they would have been able to accrue enough finances to afford the expense of such intensive therapy. The therapy took place on Adigeon Prime, a planet outside the Federation, and therefore the technicians performing the operation would have required monetary compensation, not the credits that are only good within the Federation. It has been established that the ad-hoc currency between space-faring economies is gold-pressed latinum, something the average Federation citizen doesn't usually have or need, and it is unlikely the Bashirs would have access to, at least in large amounts. However, an organization as powerful and most likely as well-funded as Section 31 would be able to afford such an operation. It had also been stated by Sloan in "Inquisition" that they had been observing Bashir for a long while. Section 31 approached the Bashirs with the offer of the operations, with the agreement that they would raise their son in such a way to be amenable to joining Section 31 when they felt he was ready. Throughout the series, Bashir mentions that his parents strongly disapproved of his considering a career in tennis and their encouragement in his decision to join Starfleet (most of their recruits are from Starfleet). His interest in spy literature may have been introduced by his parents, wanting him to have a certain romanticism towards the profession. His assignment to Deep Space Nine, a post that would seem too important for someone fresh out of school, could have been made possible by Section 31, wanting to test his skills in setting where espionage and political intrigue would flourish, especially with someone like Garak on board (and remember, they didn't know about the wormhole, and so thought this was a 'starter' position). Richard and Amsha didn't accidentally reveal his enhancements to his collegues and Zimmerman, but were ordered by Section 31 so that Bashir would be isolated and would have no one to turn to but S31. However, Richard finally came through for his kid and made that prison deal so Julian could live his life on his own terms, at least until Sloan came for him.

  • To drive this even further: What if all recruits of Section 31 are genetically altered and then raised in such a way? (Is that a case of More Than Mind Control by the way?)
    • Consider Ethan Locken, who is also genetically altered and whose catalyst for joining was instigated by S31, definitely making this More Than Mind Control. Perhaps Bashir was the prototype...

The wormhole aliens/Prophets are descendants of the Bajorans.

The Bajorans will evolve into them at some point in the future, at which point they'll exist at all times simultaneously. This will allow them to use the Orbs and, later, the Emissary to guide their ancestors' development. They are literally "of Bajor." "The Sisko is of Bajor" because he's half-Prophet and therefore half-Bajoran.

  • Political Correctness Gone Mad: Federation makes a big deal of saying "Wormhole Aliens"; Fed never says "Klingon Aliens" or "Cardassi Aliens". The Fed doesn't even say the word "Cardassians" The Federation is too busy rolling on its belly and saying to the Cardassi aliens "Take me big-boy!"
    • Because "Wormholians" would sound either suggestive, wrong or just plain silly?
    • The Klingons call themselves Klingons and the Cardassians call themselves Cardassians, so that's what they're usually called. The prophets don't call themselves anything, partly because it's really hard communicating with them in the first place, so they're given a straightforward descriptive name. If the Bajorans had a name for them without the religious connotations, they'd probably use that.
    • They are also literally an alien species, bearing little resemblance to humans in any sense. A similar example is Species 8472, who are simply referred to by their Borg designation. It happens when a species is so divorced from what humans are used to that they don't even have a concrete name for them (and the species can't or won't provide one to them) - they just give it some arbitrary designation that is descriptive in some way.

Jake Sisko is a nine-lived enchanter, and the "writing school" in New Zealand is the twenty-fourth century equivalent of Chrestomanci Castle; he's supposed to go there to train to be the next Chrestomanci.

This is why he's the only person who doesn't have a duplicate in the mirror universe.

  • Then what does it mean when he ends up not going? (It seems that the Federation is uneasy about the idea of dying for your art.)

The dim who gives Dax her combadge back in "Past Tense, Part II" is one of the hippies Kira and O'Brien encountered earlier in the episode -- and much earlier in the timeline.

Think about it. The guy's obsessed with the idea of becoming invisible -- which is how the transporter must have looked to him -- and he seems to realize that the badge (just like those ones he saw back in the sixties) has something to do with it. It's unclear how he knows aliens were involved; maybe Kira was speaking Bajoran the whole time and he wasn't privy to the translation, making it clear that her language was not of this world.

(One possible objection to this theory: he seems awfully spry for the septuagenarian he must be by 2024. But assuming a strong constitution and maybe some just-over-the-horizon advances in medical care, it's within the realm of possibility.)

Kira Nerys is a Kira.

And what is more, she is the latest of a long line of Kiras. That is why she was such an effective member of La Résistance.

This did not come out in that episode where the caste system was briefly reintroduced because what government figure would want to impose that caste from above?

  • If that was true, then why does Dukat stay alive for so long?
  • "Dukat" is a fake name. He's a Cardassian, after all.
    • Death Note works on humans only. If Shinigami have ways to kill other species, they haven't revealed them. So Kira maybe Kira gave it back when she found it it wouldn't work on Cardassians.

In the Mirror Universe, the Dominion is a democracy.

A liberal, Utopian democracy where genetic engineering ensures food for billions of citizens of hundreds of worlds. The Dominion is a powerful trading entity, it exports it genetically engineered supercrops. The Changelings walk freely among the Solids, long ago having defended them against invasion by infiltrating the invaders. There are no Jem'hadar or Vorta, they were never created.

  • No, the Vorta and Jem'Hadar still exist, but they're the result of various uplift experiments, rather than go-betweens and cannon fodder. They have full rights.
  • In the Mirror Universe, the Changelings have uplifted many, many lower life forms in the Gamma Quadrant to sapient status, and are still worshiped as physical gods by their creations. Genetic engineering is to the Dominion's utopian, liberal democracy what matter replication technology is the Federation in the Prime Universe: the technology that makes Utopia possible. It has defended the Gamma Quadrant from the Borg for at least 2,000 years, and watched the Terran Empire rise and fall from a distance.
  • So what was Mirror Odo doing at Mirror Terok Nor?
    • He was still sent out by the Founders to explore the galaxy, it just so happens that when he went through the wormhole he found the despotic, autocratic Alliance instead of the (comparatively less-so) Cardassians/Bajorans.

The Sufficiently Advanced Aliens in Star Trek: Deep Space Nine are the Force ghosts of Jedi and Sith Lords.

At some point between the two continuities, both orders died out (or decided to Ascend to a Higher Plane of Existence to prevent the Borg from assimilating the secrets of the Force -- even the Sith would have to acknowledge that they'd be unable to stop the Borg). They took up residence in a wormhole and continued fighting with each other and messing with the Muggles. Like the Force users, the Wormhole Aliens have a blue-good/red-evil color scheme, display the power of telekinesis while possessing humans, and are maddeningly cryptic about anything important.

During the Dominion War, there was a popular Klingon play written based on Glory.

Klingons would love that story. An officer helps those under him Level Grind in badass, and then he and many of them die in glorious combat.

They could just watch Glory if that work survived Earth's Dark Age -- which is dubious, given how fragile film is as a medium. But Klingons would want the story retold in the original Klingon and with the original Klingon characters.

Quark's bar is a multi-dimensional nexus.

In the Mirror Universe, everybody has a different role than in the "normal" universe - except Mirror Quark, who also ran Deep Space Nine's bar until Mirror Kira had him executed for helping Terrans escape from the station. Maybe Quark has a bar on Deep Space Nine in every universe in which a version of Deep Space Nine exists.

Another example: In our own universe, Deep Space Nine exists as a fictional station in a TV series. Quark does exist as a character in this series's narrative and has a bar on Deep Space Nine.

Darvin subconsciously wanted the crew of the Defiant to prevent him from changing the past.

That's why he made this remark about his statue having a tribble in his hand, thereby hinting at the location of the bomb.

In fact, that's why he told them the plan at all. If he'd waited a few hours, then he could have told them "You Are Too Late."

  • He may have realizied the bomb might kill or injure him if he was close enough when it went off, or that since he's a Klingon killing Kirk in a sneak attack would be very dishonorable.

O'Brien gets replaced by a replicant sometime during "Armageddon Game".

Recall that, in "Armageddon Game", O'Brien's death gets faked, and Keiko figures it out by Spotting the Thread that he never drinks coffee in the afternoon -- except, as he claims at the end, he does drink coffee in the afternoon.

In "Whispers", the episode immediately following, he's been replaced by a replicant. The replicant drinks a ton of coffee.

Keiko was right. The real O'Brien doesn't drink coffee in the afternoon. It's just that, sometime on the way back from being rescued in "Armageddon Game", he was swapped for a caffeine-powered robot.

  • Interesting, but then how does Miles have a (presumably) natural son with Keiko a few seasons later?
    • In "Whispers", the real O'Brien comes back in the end.
  • Except "Whispers" specifically spells-out exactly where he was when the replicant was made, and it wasn't the planet in "Armageddeon Game". Your theory would have been some brilliant writing, but it's more likely that these episodes were either not originally intended to go back-to-back, or nobody thought of connecting the two.

Sinbad: Legend of the Seven Seas takes place on ancient Bajor.

Sinbad's ship looks like an ancient Bajoran lightship. The gate to Tartarus is, of course, the wormhole. And Eris is probably a Pah-wraith.

The Book of Peace may somehow be related to the Tears of the Prophets.

Treasure Planet also takes place on ancient Bajor.

Morph is somehow related to the Founders. Captain Amelia is an ancestor of Kira Nerys.

Joseph Sisko spends the first few years of the show in stasis, waiting for a medical breakthrough.

Early on, Captain Sisko speaks of his father as though he was dead (though he never quite comes out and says it); sometime around the beginning of season 4, he starts referring to him in the present tense again. When Joseph appears in "Homefront", he's had a number of organ replacements and Benjamin and Jake both feel the need to nag him about his health.

We know, based on the way Bashir treats Vedek Bareil, that Starfleet medical procedure includes the option of putting a patient in indefinite stasis until their condition can be cured. Now, back in the TNG episode "The Neutral Zone," when the Enterprise ran into the cryogenic satellite, Dr. Crusher and Data referred to its occupants as dead, including those who were revived. Apparently, this applies to modern stasis techniques as well.

Presumably, Joseph Sisko was brought out of stasis during the break between seasons 3 and 4, which is why we don't hear about it on the show when it happens. Perhaps when the Enterprise-D blows up, Dr. Crusher decides to spend some time on research again...

Odo and the other changelings are the result of Instrumentality.

The Founders' standard appearance is an (attempted) imitation of the appearance of the original Humanoid we see in the The Next Generation episode "The Chase".

They look suspiciously similar. Of course, the female Founder is played by the same actress (Salome Jens), but the makeup is also similar (except for the ears).

  • The problem with this theory is that it's canon that Odo's appearance was due to him not being very good at doing faces -- and, indeed, in the episode "Children of Time" future!Odo has a slightly more humanoid (but still not perfect) face. The reason why all the other Founders look like that is because they're copying Odo.
    • What if the Bejoran people, which Odo was trying to mimic, are closer to the founders genetically.
  • In one episode, Odo is visited by another changeling, Laas, who hasn't made contact with the Founders. Laas' humanoid form appears to be mimicking whatever species he grew up around, although with an Odo-esque 'smoothness' to it, with no lips or eyebrows. And Laas doesn't have the "can't do one of your noses" excuse - he's an expert shapeshifter who can turn into fire, fog, and even a freakin' warp-capable starship. This suggests there's some 'pure' Changeling-humanoid look in there somewhere. If the other Founders were purely imitating Odo, why don't they all look like the same actor?
  • Alternatively, the Founders ARE the Precursors. All the evidence is there: they admit themselves that they used to be "solids", implying quite an old race, and they also state that they used to explore the galaxy, as the Precursors did. The Female Changeling looks like she does because she's acting as a mouthpiece for the Founders, like the Precursor in "The Chase", and that form was found to be most effective.

Eris (the first Vorta to appear in Deep Space Nine) was not really a Vorta, but something completely different.

Eris was able to beam away from the Station with no Dominion ships anywhere nearby (and we know that the Dominion does not use cloaking devices). If the Dominion had this technology, why do they never use it again? My guess is that Eris is not really a Vorta, but something entirely different.

  • Alternatively: she beamed nowhere. She's now a discorporated mass who sent her intel she gathered already. If she's a Vorta, she's basically a disposable, replaceable clone.
  • Fridge Brilliance: If you take this together with the WMG further above that Sinbad: Legend of the Seven Seas takes place on ancient Bajor instead of earth, you get... something extremely weird.
  • She was the only Vorta to ever display telekinetic abilities.
  • Maybe she was a clone of the original prototype of the Vorta species. Maybe the Vorta were originally designed with telekinetic abilities. Maybe the Vorta were originally intended to be the Dominion's footsoldiers as well as diplomats, but at some point the Founders decided that it would be better to create two weaker species which they could easily control, rather than one single "supersoldier" species: they removed the Vorta's psi powers and kept them on as administrators and diplomats, and then they engineered the Jem'Hadar as a more easily controlled species of supersoldiers without tricky psi powers that could threaten the Founders. However, every once in a while, the Dominion activated an Eris clone when they felt they needed her. She would be programmed to complete a single mission and then commit suicide in the most convenient way possible, such as by beaming into space.
  • The transporter part was Jossed on-screen: Dominion transporter was stated having range of at least three light years, when enchanched with a homing transponder like the one used to kidnap Kira and move her from Deep Space 9 to Empok Nor. Maybe she had one of those in her pocket. Still doesn't explain the telekinetic abilities...
    • As someone who features Eris in his fanfiction extensively, I think she is one of a handful of Vorta who opted for telekinesis when she first became a clone.

The Dominion didn't defeat the Maquis.

The only information we have is the intelligence gathered by Starfleet's secret service. We never see it happen. Also, it's very unlikely: neither the Cardassians nor the Federation were able to defeat the Maquis, and the Dominion isn't THAT much more advanced.

  • It wasn't a matter of tech. It was a matter of will and resources. The Federation doesn't (publicly) engage in atrocities, while the Cardassians didn't really have the resources to wipe them out and withstand the inevitable backlash from the Federation. The Dominion were perfectly fine with committing atrocities, and they could easily withstand any attack at that point. Also, one of the biggest sources was Mike Eddington, who was a member of the Maquis, and was trying to evacuate the last survivors of his cell in his last appearance.

Nagus Zek was replaced by a shapeshifter/surgically-altered Section 31 agent/surgically-altered Romulan agent sometime in season 7 -- or, alternatively, he and Quark's mother were both suffering extreme dementia.

Seriously, abdicating in favour of Rom? In the unlikely event we return to the Star Trek Prime universe continuity in the future I predict it will show the Ferengi as the alien trash of the galaxy as their world and society have imploded. This will give the Dominion/Federation/Romulans/Threat Of The Week an excuse to set up in the Alpha Quadrant again to "help" rescue Feringinar.

  • Don't underestimate Rom.
  • Let's not forget that there were distinct hints within the show's canon that Zek was suffering from dementia.

The Federation wanted to start the war w/ Dominion but found themselves outclassed and outgunned when they did.

Despite numerous warning from residents of the Gamma Quadrant about the Dominion, Star Fleet kept constantly probing deeper into the Gamma Quadrant and establishing colonies until they provoked the attack that destroyed the USS Odyssey. Then the Federation attempts a poorly planned and executed "peace initiative" that ends in its delegation being captured and "brainwashed" by the Dominion. This failure wasn't followed not by a retreat from the Gamma Quadrant, but a military buildup of Deep Space Nine.

When it was it was discovered that Dominion had infiltrated all levels of Star Fleet,the Tal Shi'ar and the Obsidian Order,the Federation did not warn the Romulan and Cardassian governments against an attack into the Gamma Quadrant (although they knew it was imminent) and thus ensured that two of their Alpha Quadrant opponents were weakened. Finally,rather than destroying the wormhole and thus preventing an attack on the Alpha Quadrant, the Federation "dithers" and allows the a war to begin w/ an enemy that,it's later revealed to have been manufacturing bio-weapons to combat against.

A conspiracy of dunces? No...a series of actions and misdirections that lead to an intended goal: A confrontation w/ the Dominion

  • Closing the wormhole was tried, but a saboteur reversed the polarity and made it too strong to destroy instead.

The Prophets didn't need Sisko to explain anything to them.

They were putting on a act in order to force him to come to terms with his own grief, because the Prophets work in mysterious ways.

Q doesn't bother the station much because of the Prophets.

When he shows up, he doesn't do anything truly Q-like--he basically annoys everybody because why not. He didn't do any truly spectacular things out of courtesy to the Prophets, who don't like other godlike beings playing in their backyard.

Commander Sisko created the Bajoran Religion.

The Prophets live outside of linear time. While they did send out probes, Cdr. Sisko is the first time any linear being responded to them. The Prophets then send out more probes to gather data; however, they appear at different time periods due to the Prophets living outside normal time. And since Sisko told the Prophets that they were of Bajor, the Prophets decided to fulfill their designated role as gods of Bajor. Some wanted to guide Bajor, others wanted to rule or destroy it; these later become the Pah-Wraiths.

The main evidence for this is the Prophets' behavior. They go from people who have no idea of Bajor to declaring "We are of Bajor," and performing various miracles that determine the course of Bajoran history (such as when they destroyed the invading Dominion fleet). There's also the sketchy evidence of the Bajoran symbol; when it is standing on end, it bears a vague resemblance to the Star Fleet Delta, with three points and a star. The reason the Prophets' behavior appears so contradictory is because they are operating outside of linear time; this allows them to meddle in Bajor's past as they grow more accepting of their apparent role as gods.

Garak "betrayed" Tain by coming out of the closet.

We're never told exactly why or how Garak betrayed Tain. (And that's good, WMG is more fun than knowing.) He himself claims he did no such thing. What if Garak came out of the closet to his father as being anything other than a healthy Cardassian heterosexual? That would be a flagrant violation of the Cardassians' most sacred belief, that family comes first, since that means Tain would never have grandchildren. (Except for those leading the Obsidian Order, I guess.)

  • That makes a surprising amount of sense.
    • Wait, didn't he have a relationsship with Ziyal? Or are we assuming Cardassian Heteronormative Crusader types, and his bisexuality was the issue.
      • Actually, in canon, while Ziyal cared for him, Garak ever saw Ziyal as a daughter, and was even a little puzzled by her affection. However, in Andrew Robinson's character novel, Garak did feel attraction to both men and women and Word of God, from Robinson and writers, who saw him as being omnisexual.
      • Both Robinson and Alexander Siddig have said that they both played up the obvious Ho Yay between Garak and Bashir until their storyline started getting dropped when Bashir bonded with O'Brien.
  • The problem with this is that Andrew Robinson decided to play Garak with homosexual subtext because he saw no reason that alien species like the Cardassians should follow human sexuality norms by default. On the other hand, that approach doesn't mesh well with the overall paternalistic portrayal of the Cardassians and the already mentioned emphasis on family and procreation.
    • Whatever Robinson's thinking, it's perfectly in character for Garak to be a non-conformist in many senses.

Garak "betrayed" Tain by confessing to someone that he is his son.

Although word never got out (the guy he confessed it to was probably killed right after) such a "blatant lie", as Tain undoubtedly would have called it, would be reason enough for a permanent exile from Cardassia.

The series does take place in Benny Russell's head

Otherwise, why would Vic Fontaine exist? A 1950's lounge singer is out of place in a science fiction show except to appeal to Russel's imagined audience. To them, having Fontaine there is the equivalent of having modern rock stars interact with characters from the future.

  • Fontaine is from the 60's, not the 50's. That aside, Word of God has said there actually was an idea at one time to have a scene at the end of "What You Leave Behind" (the finale) showing Benny sitting in a director's chair in a studio holding a script marked "Star Trek: Deep Space Nine." Whether this makes it canon or not is debatable.

Ezri's eldest brother is going through the process of becoming Joined.

At the end of Prodigal Daughter, after the younger brother was arrested, Ezri advised her older brother to "make a new life for yourself. A life of your own." She meant that he should get out from underneath their mother's wing and find out what he wants to do with his life. But since they were talking throughout that whole weekend about her having recently been Joined and the difference it made to her life, he thought she meant literally make a "new life" for himself, by becoming a Joined Trill. So he applies to be Joined and ends up being fast-tracked since his family have a history of being Joined and coping with it even without training, let alone after actually applying.

The modern day-to-day language spoken on Bajor is not Bajoran.

Rather, it is Cardassian. This can be chalked up to the Culture Police effect, most notably language suppression. It's the case with long-term occupiers throughout history, in such places as Ireland and Taiwan, and the switchover takes a generation, or less sometimes. And the Cardassians have been there for two generations. If they started immediately, Kira's generation and the generation before might well have never learned Bajoran as a day-to-day spoken language, but relegated it to use just in religion and ritual. Of course, 50 years isn't long enough to completely wipe out a language, so modern Bajoran children will probably be learning Bajoran as their primary language, as a way to recover their culture. But, just like in Taiwan, these children will probably have a hard time communicating with their Cardassian-speaking grandparents.

How can we know if this is true or not? We can't. Everyone's using the universal translator!

  • "Necessary Evil" seems to imply that Odo cannot read the Bajoran language (though curiously, Rom can), which might support this point: Odo would be trained only in the administrative language, Cardassian.

The Jem'Hadar were modified from a race with a Hive Caste System.

Specifically, they were modified from the Warrior caste and Ketracel White is based on an enzyme excreted by the Hive Queen caste (which has probably been exterminated). The Worker caste may still exist somewhere for slave labor.

Ziyal is Nerys's half-sister.

This is just a crazy thought, but it fits reasonably well. Basically, since Ziyal was born the same year that Meru died, my bet is that the death was in child birth or just happened, and that Dukat convinced the next woman he hooked up with, Tora Nepram, to be a surrogate mother for the child. Nepram never told Ziyal what the truth was, and Ziyal was given her name, so the deception was perfect. Dukat never told Kira because he was holding it in reserve to mess with her psychologically (just like how he held off with Meru), but died before he got the chance.

  • Or, following that train of thought, more likely Ziyal died before Dukat got the chance, and since Ziyal's death lead to his Villainous Breakdown he just wasn't sane enough. Although, he was evidently sane enough to tell Kira he had been involved with Meru in the first place, so maybe he was still just waiting for the right moment.

Baseball symbolizes Good.

I mean, everything about baseball including the ball itself kept being treated symbolically, right?

Sisko has Bajoran ancecestors

  • Well, he obviously has Prophet ancestors (however that might work), so who can really say? Especially if you note the WMG way up there that suggests the Prophets were descended from the Bajorans in the first place.

The Prophets are more powerful than the Q.

Note that they perceive all of time, being nonlinear. Q, on the other hand, can't, seeing as how he's "tested" people without knowing how it would come out. He also hasn't demonstrated much ability to read minds, which the Prophets do. Q's a powerful Reality Warper, but the Prophets may be more so, but are restricted to the wormhole.

  • Q is omnipotent but not omniscient. He can change form and hack reality to fit his whims. But the Prophets, while Energy Beings like Q, have a much more Starfish Alien-like psychology, being nearly unable to perceive space and time the way that humans and Bajorans do. It's not a matter of power, but rather a matter of Q being better able to readily understand humanoid life than the Prophets, who are on a different level of perception entirely.

Garak is a sociopath.

Something I've noticed about Garak when he's not in his "humble" mode. He's still polite and rather amicable. From what we've seen, whether it's torture or sharing lunch with Bashir, it's all the same to him. Not that he's entirely without morals, as we've seen him do things even without getting anything in return, but he also notably finds that behavior unnerving in himself.

Section 31 was right.

The purpose of Section 31 was to protect the Federation, whatever the means. To this end, they engineered a disease that would kill the Changelings, and infected the Great Link via Odo. This is supposed to be reprehensible, but consider that this action is what actually SAVED the Federation and stopped the Dominion. Consider that previously a group of genetically enhanced individuals had previously determined that there was no way for the Alliance to win a military victory, and that even the best case scenario, trillions of lives would be lost and the Federation and Klingons conquered. But, they were able to win because Odo offered a cure for the disease to the Founders, in exchange for ending the war. If Section 31 created the disease to wiped out the Founders, why create a cure for it? That could have been Section 31's plan all along? Infect the Changelings with a virus, bring them to the brink of death, and then offer them the cure in exchange for their unconditional surrender. Section 31, as distasteful as their tactics may have be, were ultimately responsible for saving the Alpha Quadrant from the Dominion.

  • It's Section 31's job to be right.

The Wormhole Aliens Sisko met in the the Pilot weren't the ones who opened up the wormhole

Their relationship is a lot like te Doctor and River Song. When Sisko met them in the pilot, they didn't know who he was or what linear time was. They didn't even seem to know about Bajor. After Sisko left, they sent the orbs to Bajor, ensures Sisko was born, and created the wormhole in the first place. Thus creating a Stable Time Loop.

A changeling in human form has two brains, and both are conscious.

In S03E26, Odo points out that if he's scanned while in the shape of a rock then the scan will show he is a rock. Even so, we see time and again that he retains his memories and the ability to think while he's shaped as an inanimate object. Therefore, however his his brain works, it is independent of his shape.

In the same episode, it becomes clear that some changelings can duplicate human anatomy so perfectly that no scanner can tell the difference. Star Trek scanners can measure neural activity in detail, so those changelings must have working human brains, including something that looks like thought.

If a changeling uses its (simulated) human brain to do its thinking, it will risk limiting its cognitive ability - what if the human it's impersonating is less intelligent than the changeling? It will also risk its thoughts being spied on by nearby telepaths, or even Federation technology. It's much safer to duplicate the person's brain perfectly and let it carry on thinking as if it was the person being impersonated. Hence the changeling isn't so much acting as running a full simulation of some human, and the human persona ideally won't even know. This makes the behaviour much more realistic. It also comes with some fridge logic:

Changelings do Pratchett-style Borrowing

If the (duplicated) human brain finds it's not in control of its body, it will panic, producing firing patterns that can be recognised as odd. So the changeling has to subtly manipulate the brain into doing what the changeling wants, by altering its perceptions or adding subtle suggestions to its thought processes. Pretty much what Terry Pratchett's witches do to the minds of animals they Borrow.

Changelings are sometimes mistaken for possessed humans

If a disguised changeling needs to do something it can't persuade the human brain to do, it will do it anyway - it's still the changeling's body, and it has no regard for the feelings of the brain as long as it doesn't give the game away. The brain experiences this as either a loss of control or a loss of consciousness. In extreme cases, the brain will notice parts of "its" body changing shape and acting independently.

If the changeling allows the brain to control the body again to preserve its cover, the human brain will remember these episodes and mention them to other humans. If they aren't aware of the presence or abilities of changelings, they will assume the person is either hallucinating or possessed by another intelligence.

Changelings visited medieval Earth

They impersonated humans and let the simulated brains do their thing most of the time. That gave rise to numerous legends about demons possessing people, making them do evil things, twisting their limbs and giving them superhuman powers.

Human wizards are aware of changelings, and don't trust them

Per Arthur Weasley, Never trust something that can think for itself, if you can't see where it keeps its brain.

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