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"Spock's Brain". Spock's brain is removed from his body, and his body is hooked up to remote control while the crew of the Enterprise try to get his brain back.
Rumours abound that the episode (written, under a pseudonym, by the same man who gave us Khan, Klingons and the Prime Directive) was either a practical joke or a deliberate protest against the show's new direction and producer that somehow got made anyway.
A specific rumour was that it was the writer making a rather pointed statement about Gene Roddenbery's understanding of science - or lack thereof. This probably isn't true, unless the writer was using Self-Deprecating Humor.
"The Omega Glory." We have a post-apocalyptic war between two primitive societies which threatens to create a second apocalypse. Kirk, being Kirk, takes sides. The side he takes ends up with an "American flag" and an American Constitution through some highly unlikely cultural convergence. This particular society had an illuminated Bible, which happened to have a picture of The Devil that looked exactly like Mr. Spock. They never appeared to be anything more than bloodthirsty genocidal thugs, but Kirk still took their side against their Asian-looking rivals.
"Free-dumb? That's a worship word!"
"Miri." A planet exactly identical to Earth exists in our galaxy and followed an exactly identical geological and evolutionary history right up until they accidentally create a pandemic that wipes them out. The odds of this happening should have been something like one in something much bigger than Graham's number - but Spock does say that the odds of this sort of thing happening in the Trek-verse are high. No, the problem is that the planet being an identical copy of Earth has no bearing on the rest of the story; all that was needed was a radio beacon into space and a population biologically close enough to human to pass the killer disease on to humans and half-human Vulcans. In this 'verse, that needn't be that close. The only reason the similarity is included was to give the producers an excuse to save money by re-using the sets ofThe Andy Griffith Show.
The "planet identical to Earth" silliness doesn't even have that flimsy justification — they recycled historical props and sets all the time anyway, and even hand waved it as "parallel development" in stories set on the generic-looking "class M planet" of the week.
In the otherwise good "Who Mourns For Adonais?", Kirk gives a Wall Banger speech to the ancient civilizations specialist to get her to dump Apollo, who is holding the crew hostage. The wall banger? The speech was about how her primary duty is to humanity. Good thing Spock wasn't present.
The premise of "The Naked Time" is stupid. Gravitational anomalies mutate the water supply on the Psi station to become a complex hydrocarbon that "acts on the brain like alcohol." Um... what? Why would adding a few more carbon molecules to water make it intoxicating? And the water is not "acting on the brain like alcohol." The Naked Time's first infectee's breakdown in the mess hall could be a result of that sort of intoxication (suicidal insecurities and paranoia brought to the fore from the loss of inhibitions adherent to alcohol happens); but the rest of the crew's behavior after becoming infected seems much more akin to their being pumped full of something more illicit and potent than alcohol, like PCP or Red Bull. And if it is just a "complex chain of hydrocarbons", then how the hell does it become so virulent that it's spread by touch?! Yes, the infected sweat up a storm, but getting drunk from touching them would be akin to getting drunk by screwing someone who had just had an alcohol enema anally. It doesn't quite work that way... This is likely why Star Trek: The Next Generationretconned the infectious substance into being a virus.
The episode "The Alternative Factor" stupidly exaggerates the destructive power of the normal and antimatter Lazaruses meeting in either dimension. Yes, they'd both annihilate each other; but both universes?! A kilogram of mass converts to 9*10^16 joules, which translates to an explosion of a bit over 20 megatons. Two adult bodies would be about 150-200 times that — enough to ruin your day if you're standing on that part of the planet, but a mere blip on the cosmic scale of things. Besides, don't most spacefaring species in Star Trek use matter-antimatter engines to power their starships? Yes, those explosions are more controlled than the Lazarus Nuke would've been; but they're also much bigger and much more powerful. They are also shown using antimatter as a weapon, most famously with the antimatter spread used during NextGen's "The Best of Both Worlds." And in later series (The Next Generation onward), it's established that antiparticles will explode if they come into contact with any normal matter particles of the same type, regardless of how those particles are configured into atoms and molecules; wouldn't either Lazarus detonate upon warping to the other's universe? Essentially, this one episode undermines everything that the Great Bird of the Galaxy had established and would establish for antimatter and its use in the series.
The entire resolution to the plot is a series of Wall Bangers. First, they decide that they need to trap both Lazarus inside the corridor and destroy the ship on our side which will destroy the other one and prevent reentry into either universe.
Simply destroying the ship imprisoning one Lazarus is far more humane given the circumstances we're asked to accept. It's actually a better choice since it eliminates some unknowing species duplicating the process and releasing these guys.
Kirk has to force Lazarus into the corridor and does this by wrestling him alone. Spock and 2 or 3 armed security guards are right there, but Kirk tells them to stay back. Remember that stun setting on the phasers, Jim? That might have given anti-Laz a few hours break before the fight through eternity.
After getting Lazarus into the corridor, do they destroy his ship right away? No, they beam up to the ship and then go up to the bridge before ordering the shot. Remember, there was no guarantee how long anti-Laz could hold posi-Laz in the corridor. Again, that stunning with the phaser might have come in handy.
"The Return of the Archons". After Kirk drops yet anotherLogic Bomb on another Master Computer, leaving the planet's civilization in shambles, he turns to the natives and, no lie, says: "Well, you're on your own, I hope you're up for it!" They left a sociologist, so the society isn't really abandoned, but it's a no-win situation because it invokes the old Star Trek equation "Absurdly Human Aliens = everyone follows human societal norms".
In the show's penultimate episode, "All Our Yesterdays", Spock and Bones end up trapped thousands of years in the past, and to make things worse Spock soon begins to display aggressive emotional reactions to their situation. Bones eventually surmises that because they are now in a period of time before Vulcans learned to master their emotions that Spock is "regressing" into this state too. My God man, you're a doctor, not a blithering moron!
"Amok Time": Spock goes through his mating cycle, which would end up killing him if he doesn't get off in a week. Kirk tries to convince the admirals to let him divert to Vulcan to save Spock's life, but because he can't violate Spock's privacy, he stumbles over how to explain the situation to them, ends up saying nothing, and has to violate orders in the end. First of all, Vulcans are founding members of the Federation, and Spock is a product of human/Vulcan mating. How in the hell doesn't Starfleet already know about the Vulcan mating cycle and how it could kill them if they don't satiate it? Second, even if they don't know, the ship's medical officer has already established Spock's condition is killing him. Why can't Kirk just say that Spock's suffering from an unknown Vulcan condition that he needs to go home to get properly taken care of? Certainly, without the context of the mating thing, Spock's current medical readings should be abundant medical evidence to show that something is wrong with him. Finally, even if this isn't enough to convince Starfleet to let them divert to Vulcan, Spock's father is an Ambassador there, and a prominent one, to boot. Surely they could do some name-dropping to convince them.
In "The Changeling", Kirk talks Nomad to death by convincing it that it made an error by mistaking him for its creator. Here's the problem; Nomad has already determined that Kirk is a biological unit, which it considers to be inferior, and thus refuses to believe a damn thing he says; it's already ignored several of Kirk's orders, refuted Kirk's assessment of it, and when asked how it, being a "perfect" being, could be created by an imperfect one like Kirk, gave the robot equivalent of "Don't know, don't care". Yet somehow, being told that it made a mistake in calling Kirk its creator, by Kirk himself, no less, is enough to make it go through Explosive Instrumentation. Why? How does it know that Kirk isn't lying?
Then there's the bit at the beginning, where the Enterprise gets hit with four energy blasts from Nomad that are supposedly the equivalent of "ninety photon torpedoes", yet Kirk is surprised when a single torpedo gets absorbed by Nomad.
The cloaking device. Ignoring the fact that it's already been proven such a device would make a ship easy to find (since it would show up as a huge void in the background noise, as at least one "super-stealthy" submarine crew has had the unfortunate experience of finding out), when we're first introduced to it, it's explicitly stated that the Romulans, who developed the damn thing, couldn't figure out how to see through it. To paraphrase SF Debris, how do they not know the frequency of their own damn cloaking device?!
It's never established that cloaks are like shields and get penetrated if you know the right frequency.
Captain Pike in "The Menagerie" is seriously crippled, but can communicate sufficiently to send one of two signals ("yes" or "no"). Apparently most of information theory and the concept of Morse code were lost between now and then — if he can communicate that much, he ought to be able to communicate any message... which would knock the bottom out of the whole story.
The several episodes where Kirk throws an entire planet into shambles because he personally feels that the way they live is wrong or is holding up the (wrong) concept of evolution for the people on the planet. Granted, every time the reigning person or supercomputer is trying to kill him and the Enterprise (usually for being guilty of trespassing and meddling), but when his plan succeeds Kirk then goes into some kind of speech about "how the way it was is bad and now you must learn to become proper people!".
"A Taste of Armageddon" has the Enterprise caught between two planets that are fighting a war with computers. The computers count casualties and the people report to desintegration chambers. When one planet falls short due to the Enterprise crew refusing to report, the other planet knows about it and prepares for a real war. Unless this is all some population control scam, it makes no sense. The two worlds agree enough to construct an elaborate interconnected war simulator and agree to not launch real weapons at each other. Wars tend to be about territory, resources, and ideology. Killing people is more of a side effect of a real war. Destroying the other side's infrastructure is the point. If the two sides could agree on this system, how could they not just agree to stop the war? They've already gotten past the hard part.
Except that, in the story, it's said that both sides started with the premise that their species are basically warlike and that true peace is impossible. So, they just decided not to waste time on it and just go with their warlike nature in as clean and efficient a way as possible. Kirk just points out that maybe they should at least try to give peace a chance.
From "The Enemy Within", Sulu and some Redshirts are stranded on a planet with the night time surface temperature dropping rapidly, yet are unable to be beamed aboard without having their good and evil sides split apart, as shown with Kirk. It's some good drama, but there's a problem: Why couldn't they use a shuttlecraft to pick them up, or at least explain why they couldn't do that to help the guys trapped on the planet? The subplot is, at the end of the day, just a means to add some drama to the story. Oh well, at least the main plot is strong enough to greatly pick up the slack.
There is a very reasonable real-world explanation for this: The creators hadn't actually come up with the concept of shuttlecraft yet. We wouldn't see a shuttle until The Galileo Seven which was 9 episodes after this one.
The ending of the episode Assignment Earth. The story goes that an alien race kidnapped humans from Earth and trained them to be soldiers fighting the good fight in an effort to save the Earth. One such man is Gary Seven, on a mission to stop the United States launching an orbital weapons satellite into orbit that is armed with Hydrogen bombs - a mission that he succeeds at by blowing it up at launch with the aid of Kirk and Spock. Now normally this would be the end of it; potential nuclear holocaust averted, job done. Or it would be if it wasn't for a small piece of throwaway dialogue earlier in the episode from Spock that categorically states the launch of this weapons platform is to counter the launch of another such weapon by other powers (obviously the Soviet Union as they were the only other space capable power in 1968). In other words, by focusing solely on the US satellite instead of aiming to stop them both at once, our heroes have essentially allowed the Soviets the ability to circumvent just about every form of nuclear defence system the United States possesses. Pretty shrewd move a mere six years after the Cuban Missile Crisis huh?
Gary Seven's origin story also qualifies: Taking children from Earth and training them in the use of your advanced technology in order to protect the human race from itself? Absolutely believable. Taking children from Earth six thousand years ago? Absolutely absurd. What possible reasoning would they have had to think the human race was progressing too fast for its own good when we had barely perfected farming by this point?
This has led to theories that Seven's bosses had the ability to see into the future. In addition, Seven says that the humans and their descendants were trained for generations for their task. In the episode itself, Scotty speculates that Seven's transporter beam might've even brought him there from the future. This has, itself, led to certain theories about Seven's bosses occasionally using someone else as an agent.
Worse, Worf causes millions of credits in damage, throws his lot in with these punks, and goes along with this crap because he's in a jealous snit over a relationship his then-new girlfriend's past life had with another woman. Jadzia, seriously? Would have thought you'd have better taste than that.
The second large but often overlooked wallbanger of the episode? Curzon Dax; best friend to the future Emissary of the Prophets, mentor to Jadzia, ambassador who represented the Federation at the Khitomer Peace Conference and highly respected friend and ally of three of the greatest warriors the Klingon empire has ever produced? Died during some obscure sex act. Way to ruin the death of such an accomplished man, guys.
"Profit and Lace." Quark gets a sex change operation, which in the 24th century apparently involves brain surgery to make the patient start behaving like Betty Crocker.
"Sons of Mogh": An atypically Jerk Ass Captain Sisko meddles in Worf and Kurn's private affairs by saying Kurn is not allowed to commit assisted suicide, which is perfectly lawful (and, if you've been dishonored, recommended) under Klingon law. This despite both Captain Picard and Captain Janeway having allowed people the choice in the past. That's right, there is canonically an issue about which Sisko is less understanding than Janeway...
The difference is The Sisko is administering a Bajoran station under Bajoran law, not a Federation ship under Federation law like Picard and Janeway. If Bajor has a prohibition against suicide (or sees assisted suicide as murder) then as long as Kurn is on the station no killing self! Although this could be gotten around by The Sisko just putting Worf and Kurn on board the Defiant and sending them out of the system.
The episode's solution to this problem is arguably worse. Without Kurn's knowledge or consent they give him plastic surgery, alter his DNA and wipe his memory so he thinks he's the son of one of their family friends who takes him in as his own son. Moral of the story; suicide is wrong but brainwashing people is A-OK as long as it's for what you think is their own good. Plus in later seasons Worf regains his honor and becomes a hero in the Klingon Empire while for all we know Kurn is still brainwashed.
They establish that the brainwashing is irreversable, and Kurn's old personality is gone forever. Which means that they avoided killing Kurn by... killing him. Babylon5 spent two whole episodes dealing with the morality and consequences of "death of personality" but here it's done in 1 minute and everyone is somehow happy because Kurn's not dead... even though he is, and a stranger now wears his face. *BANG*
Season seven: We have the wormhole closed at the end of season six... and apparently this leads to things going south for the Alpha Quadrant forces even though the Dominion are based mostly on the OTHER side of the wormhole AND had an entire fleet of reinforcements disappeared by the Prophets in mid-season six. Apparently, Sisko opening the wormhole again INEXPLICABLY turns the tides of battle (shown gratuitously), thus showing that superbeings were helping the good guys win. Which likely was the point, but the Skepticism Failure is painful.
And the season seven finale... which had considerable clip content... sigh.
Sisko once let Jadzia Dax go out and fulfill a Klingon Blood Oath. StarFleet might be Mildly Military, but letting an important officer go out and kill people for no reason but revenge (Jadzia wasn't bound to the Oath in the beginning — it was made by the previous Dax host — and she wasn't even a Klingon) is simply insane.
The sad thing is, her keeping that oath for Curzon Dax proves critical for the plotline of the rest of the series. Because she does it, she becomes an honorary Klingon; because of this, Worf gets another chance to be a legal Klingon, and the Klingons remain allied to the Federation (with Jadzia as liaison)... Her running off to do something that should, by Federation standards, be outright immoral, which is in itself nothing more than vengeance, is critical to the resolution of the Dominion War!
The entire command staff had a tendency to leave at the same time, and no one ever thought this was a bad idea. When the station commander (a major religious figure), the security chief, the chief medical officer, the first officer (the liaison with Bajor) and the chief of engineering all leave at once, who is running the station? Nog? Morn?
That's a problem with nearly every show like this. TNG had this less, in part because Riker liked to remind Picard that captains aren't supposed to go on away missions. But generally, the cast are the ranking officers, and the scripts have the cast in the thick of things. And Deep Space Nine is worse than TOS or TNG when it does this because there's so little redundancy — it is possible that the main cast contains everyone on Deep Space Nine proper with any rank in Starfleet.
In the finale of the third season of Deep Space Nine, Sisko initiates the self-destruct system on his ship because an alien has co-opted the controls and may cause a war with some other aliens. (Long story) But WHY does Kira have the self-destruct code to confirm this? She doesn't belong to the Federation — her authority shouldn't extend past Deep Space 9 itself. For that matter, why are Odo and Kira on this ship? They're not in Star Fleet! They have authority on Deep Space Nine because it's a Bajoran station (Kira chose to grandfather Odo in); but they have no reason to be on a Federation ship In-Universe. It's just to keep the ensemble together for the episode — and the problem with that is noted above. (To rephrase: Who's running the station?)
Kira is attached to the Federation and her authority extends to being a 'loan' officer, much like that episode where Riker became a Klingon Officer. They give her fully rank and privilege because that's the entire point, that she is shown to be an equal partner in the Starfleet Mission for Bajor.
"Q-Less": To sum up, Vash, one of Picard's love interests from a previous episode of ST: TNG ("Q-Pid") is found on a planet in the Gamma Quadrant. From that point on to about 20 minutes into the episode, the two big questions are "how did this woman get to the Gamma Quadrant without the wormhole?" and "why is this completely intact runabout nonfunctional?" Now, keep in mind O'Brien from TNG, who happened to be present for the events of Q-Pid, is on the station. Sisko asks him directly about Vash; he tells Sisko about her history with Picard and nothing else. Sisko continues to worry about this possible security breach, and O'Brien continues to have problems with the runabout and soon, other power drains on the station. This state of affairs continues until O'Brien sees Q at the cafe. He then immediately tells Sisko and adds that the last time they met, it was with Vash in Sherwood Forest ON THE ENTERPRISE. Can we put two and two together? As soon as the ship came in with the unexplained power drain and the woman who just magically appeared in the next quadrant over, who by the way was involved with a Q, O'Brien should have realized what was going on and told Sisko, who should have then either told Q to show himself and state his business (just like Picard would), or put Vash on the next shuttlecraft or runabout back to the Gamma Quadrant. Starfleet should not have to defend humans who willingly make deals with Q from the Q Continnum (especially after Picard told her You'll Be Sorry).
But then we (probably) wouldn't have the awesome scene of Sisko PUNCHING Q.
"Chimera": In this single episode, another lost Changeling demonstrates that Odo's race are capable of shapeshifting into gaseous forms, expanding to fill large areas of the station, transforming into FIRE, and becoming an organism capable of traveling unprotected through space at Warp speed. Now, Odo's race is powerful, and the one in "Chimera" is unusually powerful, but this violates Willing Suspension of Disbelief.
"The Darkness and the Light": Imagine a story where some poor schmoe is minding his own business, not hurting anybody, and then some terrorists plant a bomb that explodes and horribly wounds him and scars him for life, as well as killing a lot of other innocent civilians. Now imagine that the victim recovers and goes on a Roaring Rampage of Revenge against his attackers. We're supposed to be rooting for him, right? WRONG! Because, you see, the person who planted that bomb happened to be Kira Nerys, and therefore this Cardassian is a bad, bad manbecause Kira is one of the good guys. And when he tells her about all the pain and death she caused to Cardassians who never lifted a finger against her or any other Bajoran, she loses her temper and screams at him that he was guilty just for being there. According to Memory Alpha, Ronald D. Moore said "You can't say whether it's right or wrong – it's the stance of a terrorist." Fuck that shit! You absolutely CAN say whether it's right or wrong, and it's so wrong it's off the fucking charts! After seeing this episode, if they had killed off Kira later in the series I would have cheered myself hoarse.
Except for that whole "brutal enslavement and occupation" thing. If she had done it on Cardassia, it'd be outright wrong. On her own planet, currently under occupation by a foreign power exploiting it for resources while being as close to a Nazi allegory as you can get, not so much.
Agreed. When you remember that the Bajorans had "never lifted a finger" against the Cardassians before they started being annihilated, the ambiguity of this issue is validated. Besides, DS9 was always MEANT to have darker storylines and characters with messier moralities. Kira is not a Starfleet officer. She is a freedom fighter who has been trained to hate and kill for her entire life. She can't just apologize for helping to liberate her planet, much less so at the drop of a hat, and ESPECIALLY not when the person who thinks she should be apologizing has just killed her closest friends and is about to rip her unborn child right out of her.
Doesn't that pretty much throw away the point of Duet?
It would have if it happened after but the whole bombing affair happened years before Duet. During this episode, Kira is just high on revenge and didn't want to justify her actions to the murderer who killed several of her friends. Besides, it's shown she thought he was right to some extent, considering the behaviour she adopts afterwards.
Also, Duet showed Kira moving from categorically hating EVERY Cardassian to only hating those involved in the Occupation of Bajor, and even then finding the ability to forgive some of those occupiers. The tragic figure in Duet earnestly regretted his inaction as a clerk witnessing such horrors and had tried to make penance. The figure hunting down Kira and her friends for revenge saw his noncombatant status as a shield of innocence that the Bajorans violated; reasoning which Kira hotly rejected.
Kira: None of you belonged on Bajor. It wasn't your world. For fifty years you raped our planet, and you killed our people. You lived on our land, and you took the food out of our mouths, and I don't care whether you held a phaser in your hand or you ironed shirts for a living; you were all guilty, and you were all legitimate targets!
"Sons and Daughters": Despite ever showing any interest in becoming a Klingon Warrior, having no combat experience, training, minimal knowledge of Klingon culture AND a personality that could make Hinata Hyuga feel pity for him, Worf's son Alexander not only manages to get a job in the Klingon defence force but also manages to get a job on General Martok's Bird of prey; which is the real world equivalent of a convenience store clerk getting a job with the Marines Corps. If he had been on any other Klingon ship, Alexander would have been dead within a week.
Well, despite how much they go on about honour, Klingon society is rife with corruption. He probably got posted there due to nepotism. IIRC, Worf was on the ship at the time.
It's actually quite easy to picture the recruiting officer telling himself this sorry excuse of a Klingon will get himself killed in a week if he doesn't have his father behind him to watch over his shoulder.
Any time there is a shipwide/stationwide issue with transporters, where someone's life depends on having one, and everyone forgets about the transporters on the shuttles/runabouts. Most of the time when this happens, the issue is needing to beam someone off the surface of a planet from orbit, something we know shuttles and the like can do. Oftentimes in this situation, conflict and tension are produced by having the ship experience some shipwide failure or damage that is keeping the transporter system from working, usually something like battle damage, or less commonly, a computer malfunction. In these situations, no one thinks to run down to the shuttle bay and use the shuttle's transporters? While this wouldn't help in situations where there was an honest to god force field or something blocking the transporters, it would solve situations where the transporter was simply offline immediately. In fact, that this can be pointed out at all suggests that maybe they should have an emergency transporter that isn't physically connected to the ship in any way, just like one can have a generator that isn't connected to a building's power supply.
The Changing Face of Evil: Kai Winn's most trusted advisor discovers that her lover is in fact Gul Dukat, disguised as a Bajoran who died years ago in a labor camp. Dukat, besides being a mass murdering megalomaniac who is responsible for countless deaths on Bajor, has convinced Winn to obtain a number of books that are considered to be so evil that even looking at them is banned. Armed with this infomation, what does this advisor do? Does he a) bust in with 50 members of Bajor's finest and most heavily armed soldiers, to arrest this war criminal and put an end to any demonic plotting he may be up to, or b) go up to Kai Winn's room alone, and tell Dukat and Winn that he knows what is going on and who Dukat is? Well, if the advisor had done a), the series finale would have been an hour shorter, so...