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Star Trek: Enterprise damaged its credibility the moment it became clear that the communicators didn't work as well as the transporters. Working "cell phones" were beyond 22nd-century Starfleet, but disassembling living and non-living matter down to the sub-atomic level, flinging it vast distances, and having it reform perfectly was no problem. Seriously?!
It's strange when you consider that many of the big transporter screw-ups happened in series that come later in the universe's timeline. Starfleet should have improved and perfected the technology. This is an overall, retroactive Trek wallbanger.
The "decontamination gel" is simply idiotic any way you look at it. It's supposed to be rubbed all over the body. What about the privates? Shouldn't the away team be completely naked? (You'd have to aim the camera carefully, but...). It also seems that away team members aren't able to rub themselves with the gel. Instead, they have to rub one another. What would they do if only one person leaves on an away mission? Who would rub them when they come back? A decontamination shower would not only have made more sense but also have been more titillating.
The episode "Dear Doctor" has Captain Archer and Denobulan Dr. Phlox withhold a vital antidote intended for an alien humanoid race dying of a serious disease. They elect to cause genocide because of a set of rules (that is, the Prime Directive) that might be instituted in the future (Archer only just came up with it!) and because a second sentient humanoid race on the planet might be better off if the first race went extinct. Never mind that it lacked common sense; it also made them look like mass murderers. Interestingly, John Billingsley (who played Phlox) noted in interviews after the fact that he didn't agree with the ending for the episode, noting the above.
Look like??
The entire premise that the first race was somehow "holding back" the evolution of the second race simply by existing was utter rubbish. It was an unpleasant "parents must die for the children to reach their full potential" Aesop. Biologists long ago dumped in the trashbin the idea of an "evolutionary plan", which by some unseen hand (* cough* ) progresses the evolution of species from a "primitive" stage to its destined glorious pinnacle, with Mankind (especially white people) standing tall at the top of the Great Ladder. (Manifest Destiny, indeed!) The idea is and has long been popular in Sci Fi, but anyone espousing it clearly demonstrates that he doesn't understand what Darwin and modern evolutionary biologists are talking about! Evolution is not some inexorable "progress" to higher levels; nor does "mutation" and genetic drift work like a magic wand.
The second race had started with ape-like intelligence and had been fostered by the first race. They were getting more intelligent while coexisting with the first race. This was cited by Phlox as "proof" that the second race was trying to fulfill its "genetic destiny" (what?) and the first race was holding them back. It's far more likely that the second race was becoming more intelligent because of coevolution with the first race and their high-tech civilization - they were subtly being bred for it, just as 15,000 years of coevolution of humans has increased canine mean intelligence (compared to wolves). Apes held in captivity to be taught sign languages have been documented to teach sign language to their own children and other apes, both in captivity and after reintroduction to the wild! What kind of pressures to adapt to human presence does hunting and habitat destruction put on chimpanzees?
If they never wanted to get involved, then they shouldn't have promised to help, created a cure, and then changed their minds and left only a hint. That was heartless. And then, in 'Observer Effect,' they have the audacity to cry and whine about the Organians sitting back to watch them die!
In "Observer Effect", how does increasing the risk of infecting your entire crew and then deliberately exposing yourself to something you know will kill you before you can cure it to "help" two people who are already dead help anything? It's idiocy bordering on retardation... or perhaps that's the kind of "special" they meant.
Season Three brought Seasonal Rot to a whole new level by retooling the series to be 24IN SPACE!, minus the real time. "Chosen Realm" was one of the most insulting, trying to act as a metaphor for the 9-11 attacks - the Enterprise is hijacked by extremists with "Organic Explosives". It turns out that the only reason that the Enterprise was hijacked and people killed was that these terrorists had a feud with another faction about whether the Spherebuilders made the Universe in six days or seven. Wow. That kills the analogy. At least with 9/11, we know that al-Qaeda was (and is) angry at America itself...
Worse, until the reveal about why they wanted to steal the ship, the episode provided an interesting look at how religion can make otherwise nice people do terrible things, as the hijackers do indeed express distaste for what they are doing, giving us the impression that what they are doing is an act of desperation. The reveal takes that away by showing that the hijackers are not otherwise nice and reasonable people, whose religion has driven them to desperate acts of violence, but hateful, petty bigots, who lose any sympathy with the audience.
Hell, Season Three was just incredibly distasteful, even going beyond the ham-fisted War on Terror allegories. The entire fucking premise of Trek is "let's see what's out there". It is NOT "let's see what's out there and kill it before it kills us". Ugh.
The fourth season premiere had the Enterprise become indirectly responsible for creating an alternate Earth populated with evil space Nazis (and they are different from the space Nazis seen in an episode of the original series). The entire Temporal Cold War arc is dropped with little explanation.
The "reason" that the Temporal Cold War was dropped is that, somehow, the time/space Reset Button was hit and somehow it was the Space Nazi leader going back in time that started the Temporal Cold War...which one is best not trying to justify. It, like many time-travel related things, makes progressively less sense the more it is analysed.
Daniels spent the entire previous season trying to dissuade Archer from taking unnecessary risks. Why send him into a deadly situation without giving him a chance to prepare for it? If you can send anyone, from any point in the history of the universe, to be your temporal agent deputies, then why not send someone whose ship is a match for the Space Nazis' technology?
Why did the Space Nazis align with the Nazis? They needed to form an alliance with a local power so that power would give them resources, yes. But the USA, the USSR, and British Empire were all richer in the kinds of resources they were asking for than Nazi Germany. Also, since the Allies won--and the aliens had no reason to care, since one of their goals was to wipe out ALL humans--and since the aliens, who have a time traveler's categorical knowledge of history, knew that the Allies won, they should have just given the Allies some cool guns and sent them on their way. By joining with the Nazis, they not only needed to give the Axis cool guns but also had to waste energy figuring out how to manipulate the timeline to change the outcome of the war.
The finale of the show is a Star Trek: The Next Generation episode in disguise, completely ignoring both shows' continuity and characterizations. The worst offender? Trip Tucker blows himself up during a hostage situation. Not once does he think to wait for a security team to arrive (T'Pol alerts everyone to intruders on the ship), nor does he try to stall for time. Instead, he has the aliens knock the captain unconscious and then leads them to a room where he intentionally blows himself up...and for what? (There is an officially licensedFix Fic out there.)
Is anyone surprised that the Xindi managed to blow up their home planet? They're CONSTANTLY bickering amongst themselves - they bicker so much that their council is no more effective than the UN. And they spent huge amounts of resources on a superweapon to destroy a planet - which is stupid for many reasons for any civilisation that has warp technology. Not only that, when they're duped into thinking that humans are their enemies and they have to destroy them... instead of testing their mini-death star on, say, a barren rock or moon somewhere in their own backyard... what do they do? Yup, they send it straight to Earth, tipping their hand, when, if they had tested elsewhere, they could just have dropped the finished superweapon out of warp on Earth's doorstep and KABOOM! Also, literally millions of people are killed in this pre-emptive strike on Earth, and the Vulcans are Earth's first and closest allies, but come the finale, who helps out Enterprise? Andorians (whom the Vulcans are unfond of). Perhaps Archer's racism pissed them off enough that they wanted humanity to die. It seems logical.
You would think that logic would have told the Vulcans that someone sending a baby Death Star to Earth would warrant, if nothing else, a number of Vulcan ships in case anything went down... but then, even a few hundred years later, the Federation seemed to have precious little in terms of Earth-based defences.
Archer pissed off the Vulcans by incidents like P'Jem. It's understandable that the Vulcans regard the Andorians, a real challenge to the Vulcan space power, as a higher priority than guarding some insignificant, unreliable ally such as Earth.
The Xindi as a race (originally) comprised six humanoid aliens that come from such taxonomically disparate groups as reptiles, birds, mammals, insects, and "aquatics". But we're told that they diverged relatively recently (somewhere in the order of tens of thousands of years), are all the same species, and are genetically MORE similar than humans and chimpanzees. Now, it's true that they aren't 'technically' reptiles, birds, mammals, insects and fish, but we're expected to believe you could get that much variation in biology in less time than it took humans to go from 'short and hairy' to 'tall and bald', and with less genetic difference.
This one could be traced to TNG's "The Chase."
The episode "Bound" is full of Wall Bangers. Long story short, the Orion Syndicate has put a bounty on the crew of the Enterprise, and an Orion bounty hunter comes to collect. He does this by giving the crew three Orion women, who have the power to control men and weaken women with their pheromones. It's discovered that the women are controlling the men and using them to sabotage the Enterprise so that their "master" can come and capture them without incident. Captain Archer is trying to interrogate them, but is so enthralled that he can barely keep his head up and his eyes forward. He almost lets them out of their prison cells upon request, and he would have if it weren't for T'Pol being right there. He then goes back to the bridge, leaving them with a single male armed guard. Ten minutes later, they're out of their cells and the guard has taken 5...
Didn't it occur to anyone - the captain, T'Pol, Trip (who wasn't affected due to events earlier in the season) or any female member of the crew (we have a female communications officer) — that maybe they shouldn't have women who can make men do whatever they want be guarded by men?
T'Pol was slacking off on her Straw Vulcan duties. The instant it was discovered what effect the women had on the men of the crew, she should have immediately relieved Archer of command - by Vulcan Nerve Pinch if necessary. A few of the men were clear-headed enough to understand and go along with this almost to the end of the episode.
Are there no rooms with separate ventilation systems on the Enterprise? Can't they filter the pheromones out of the air? Or put the Orion women in a big soundproof box with an opaque door or force field so they can't seduce anyone else? This makes less sense because Expanded Universe prisons are often literal boxes with life support that you are beamed into and out of for visits. Okay, so Star Trek's Expanded Universe isn't canon (not even the licensed parts), but couldn't the writers have at least taken a cue from it?
The biological changes made to female Vulcans and Orions are particularly noteworthy because they are technically Star Trek's two oldest species, mentioned all the way back in the 1963 pilot. The ideas were Canon Immigrants. The reasons for making them up or making them canon were very likely these: Wouldn't it be awesome if every big boobed, incredibly attractive supermodel in the universe was compelled to have sex with you no matter how ugly you were? ooh! and what if they had pheromones that made you their sex slave... wouldn't that be awesome?! No guys, it wasn't.
That isn't even half the problem. Would T'Pol have been required to return to Vulcan and fight with an axe like the males? If both sexes have Pon Farr, how come males have to fight themselves if it doesn't go smooth, but females can pick someone to do it for them?
In "Zero Hour," Archer, Hoshi, Reed, some MACOs, and some Xindi councillors who have gone over to the good guys' side are preparing to board the Xindi weapon and destroy it from within, but whoever's monitoring the skies over Earth has no way of knowing that (since Archer hasn't been seen to file a report). They destroy the weapon, and the events of "Storm Front" happen. At the end of that arc, the Enterprise is greeted by a number of smaller ships. The question is: where were these ships during "Zero Hour", and why didn't they participate in that battle?
"Regeneration" has been criticized by fans for having the plot make several ridiculous concessions in order to justify the crew fighting the Borg in the 22nd century - and not just any Borg, either. The plot of the episode involves the wreckage of the downed Borg sphere from Star Trek: First Contact (who destroyed part of a fleet in that film) being discovered in Antarctica by Starfleet researchers. Said wreckage happens to contain still-active drones, who assimilate the researchers and a ship before being stopped by the crew. However, this leads to several retroactive wallbangers:
The crew interact in several ways with the Borg: they hear an audio communication from them (conveniently omitting the iconic "We are Borg" designation), they have nanoprobes obtained from Dr. Phlox and there's wreckage from the ship still present in Antarctica. Why, then, is none of this data (and there's a lot of it) factor in any way into the later Star Trek series like Next Generation (when the crew first discover the Borg)?
Despite having vastly inferior technology and weapons at that point in the timeline, Phlox is able to successfully hold off the Borg nanoprobes he's been injected with and provide a countermeasure for it (though admittedly a highly dangerous one), something even Beverly Crusher couldn't do 150 years later. Meanwhile, Reed gets many more shots off with a simple phase pistol than current-era phasers do, and he wasn't even smart enough to rotate the frequency. He just gave it more power.
What is wrong with Archer in "Fight or Flight"? He is fully aware that his ship's armaments aren't working the way they should, he has no idea how powerful the hostile vessel is[1], he has no idea what the circumstances were that led to a ship's crew being killed[2], his crew has very little practical experience in space combat and his best officers think it's a bad idea to go back. He still decides to put the ship in serious danger for no reason whatsoever.
Fortunate Son marks a rather impressive moment of utterly frustrating idiocy, as Archer insists that the Enterprise must stop human freighters that are constantly being attacked by alien pirates from doing anything to defend themselves, because self-defense against pirates is wrong.
To make matters worse, several people very effectively call him out on how out of touch with reality his decision is, and he doesn't give any real answers to their objections beyond acting like a smug jackass.
↑ for all he knows they were criminals in a strange execution. Or mind-controlled slaves of Shapeshifting Space Bogeymen Of The Week - which in Star Trek 'verse seems to happen often enough to be in the first 3 guesses for any and all weird incidents.