Accidental Innuendo: Trying to befriend Chakotay by getting to know his beliefs better, Janeway learns about spirit guides. While it's clear she's referring to Chakotay's spirit guide, she asks Chakotay if he's a bear.
Kathryn Janeway is subject to a lot of this. The writers of Voyager were notorious for not liking the show that they were writing for very much (understandably), and not agreeing on the interpretations of certain characters. Janeway was the worst example of this. Some writers wanted to cast her as compassionate and motherly. Other writers wanted to depict her as a consummate professional. Still others wanted her to be a tough-as-nails bitch. As they each took their turns trying to morph her into these archetypes, they often went overboard, perhaps in an effort to "make their point" or to "solidify" the character trait which they favored. The result was a character who was a total mess; erratic, inconsistent, and seemingly irrational as she behaved in the extreme ways dictated by her position as proxy for the bickering writers, resulting in wildly varying fandom interpretations:
Generally speaking there are two interpretations of Janeway: The self-flagellating, steely-but-compassionate woman who is doing everything in her power to get this crew back to their families, and one who is... not.
Or was it just manic-depression? For instance one episode, "Night", has the crew suffering from a severe drop in morale, thanks in large part to Janeway having locked herself in her quarters, with the lights off, for two months and refusing to communicate with anyone but Chakotay. She's the very picture of mental health! The two-parter Borg episode, "Scorpion", touched briefly on Janeway's emotional turmoil over stranding 150 people in space over a mistake. She was willing to lend aid to the enemy if it meant surviving Borg Space, something that Chakotay was not prepared to do. It didn't help that the character was written with a dartboard, making the mood swings incidental at best. According to Kate Mulgrew when asked during an autograph signing, she said her belief was that Janeway was in fact at best bipolar or at worst, suffered some kind of mental instability.
Meanwhile, The War of the Masters (a Shared Universe on the Star Trek Online forums) interprets her as simply having been put by circumstances into an position well above her skill level. The 'verse further interprets her promotion to flag rank in Star Trek: Nemesis with the common fanon assumption that she had been Kicked Upstairs to keep her out of any further field command.
Chakotay's fictitious tribe features traits of various native peoples ranging from North, Central, and South America and even New Zealand (their cultural advisor notoriously lied about his qualifications and learned everything he knew from Hollywood Indians). Fans of the character, who is said to be from a Federation colony on the Cardassian border rather than Earth, sometimes interpret his true culture to be a newly formed one unique to the 24th Century, a sort of New Age revival movement.
Chakotay is revealed in "Shattered" to have a hidden supply of cider in one of the cargo bays for the last seven years. No wonder he comes across as being wooden, spouts nonsensical mysticism at the strangest times, has questionable command abilities, and for the life of him can't land a shuttle without crashing it into something! It's entirely plausible that he's been secretly drunk for the entire trip. Although to be fair, if you were in Voyager's position—trapped on the opposite side of the galaxy, forced to work with the people who you were fighting against, assuming your people back home are being wiped out by the Cardassians, decades from resupply, knowing you'd never see home again, the imminent threat of cyborg zombies hanging over your head and with a very questionable person in charge—would you honestly be able to handle it without either going nuts or getting drunk?
Where did he get the cider? All of his personal effects would have been on the Maquis ship when they were brought to the Delta Quadrant, and no one would take the trouble to beam out things-that-weren't-people-whose-lives-needed-saving in the middle of a battle before the ship was destroyed.
Chakotay's not the only one who might have been intoxicated. Kes constantly sees visions that no one else can see, and speaks in an oddly calm, half-there tone of voice. Kes has a little garden where she grows exotic plants. Coincidence?
One interpretation of Harry Kim is that he's a severely repressed homosexual who deliberately seeks unattainable women in order to vastly overcompensate for his unrequited love for Tom. This would explain a lot.
Consider for a moment that the Kobali from "Ashes to Ashes" simply couldn't have evolved to reproduce via necromancy and apparently had no difficulty traversing the 30,000 lightyears crossed by Voyager since Lynsday Ballard died, it makes more sense to speculate they're members of an insane cult that was driven off their homeworld and now is constantly moving, to avoid the countless alien authorities who've taken exception to them profaning their dead?! Given Janeway's rather dubious track record over the course of the series, one could even suggest they're following in her wake! Alternatively, they were never a naturally-evolving species in the first place, but rather a Frankenstein-style artificial population that broke away from their creators and established their own civilization. For its part, Star Trek Online (non-canon) gives a handwave that the Kobali were messing with "forces beyond their control", implying they screwed up their own genome.
The fact that the Ocampa can only procreate once in their lives has led to the assumption that they normally produce litters (as otherwise every single one - including males somehow - would have to become pregnant in every generation to maintain zero population growth).
Species 8472. Considering they were fighting the Borg in self-defense (as do everyone else the Borg have come in contact with) and that we have only the word of Kes and her unreliable Psychic Powers that Species 8472 were Omnicidal Maniacs, "Scorpion" has been accused of Protagonist-Centered Morality and Janeway of treason against the Federation in aiding the Borg against them (as well as disobeying standing orders, given TNG: "Descent"). It's also unsurprising that 8472 would be angry enough at the Federation for her interference to have switched their primary target away from the Borg by the time of "In the Flesh". Janeway has also been accused of Fantastic Racism in her dealings with them, since she went straight to the assumption that they were worse than the humanoid Borg with little evidence when they were non-humanoid tripods, but was suddenly open to peaceful negotiation (even quoting the regulation she should have followed back in "Scorpion"!) when they took human form.
Base-Breaking Character: Neelix got this bad. A lot of very young Trekkies supposedly loved him and his endless supply of cheer and goofball charm (though that's certainly not universal). Many adults found him boorish, incompetent, and overbearing (his fumbling of duties in "Basics Part 2", resulting in two deaths as a direct result of his incompetence in a field that he claimed expertise in, being a major target of scorn). His hatedom is second only to Wesley Crusher in Trek circles, yet he doesn't quite count as The Scrappy since kids loved him so much, and it is worthy of note that later seasons smoothed out his edges a bit ("Once Upon A Time" even had the actor add in a little bit where Neelix looks surprised that anybody could genuinely be happy to see him).
The writing crew were aware of Neelix's base-breaking tendencies, and the season 2 episode "Parturition" was intended to be an Author's Saving Throw, written solely to put the kibosh on an unflattering Love Triangle arc with Kes and Tom. That didn't quite work as planned - it resulted in Tom Paris being a mature adult while Neelix spent much of the episode being hateful towards Tom because of his psychotic jealousy.
Due to the inconsistent characterization and some questionable decisions, Kathryn Janeway is probably the most base-breaking of the Star Trek captains, with a significant hatedom contrasted with a diehard fandom. See Designated Hero below.
Best Known for the Fanservice: Seven Of Nine got one of the show's best character arcs and was the focus of many well-liked episodes, but let's get real here - to much of the audience, Seven and her Stripperific catsuit fell under this trope.
Bizarro Episode: "Threshold." The crew's latest go-home plan involves a drive capable of infinite speed, which when tested on a shuttlecraft prompts Tom Paris to mutate into a giant space salamander, kidnap Janeway, turn her into a salamander too, and settle down on some random planet to have space salamander babies. It's small wonder no one ever mentioned it again. Plus, at episode's end they actually have a way home, and a cure for the problem it caused.
Jeri Ryan (Seven of Nine) and Robert Picardo (The Doctor) are so multi-talented that they can carry the entire show by themselves, as they have shown on repeated occasions.
Picardo has the Midas touch. The Doctor is simply the best thing about Voyager (beyond some sterling moments with the female cast), and one only has to take Picardo and inject him into a sister show (DS9) or movie (First Contact) for brilliance to be assured! The Doctor was easily the most consistently-written character, and one of the few who actually evolved over the years.
There's a great TV Guide interview with Ryan from when she first joined where she stated skin tight catsuits and nine-inch heels = Masterpiece Theatre acting.
Neelix was supposed to be this, and was advertised as such early on, but it didn't work out.
The episode "Course: Oblivion" is either regarded as one of the best episodes of the series for its brutal gut-punch of an ending, or one of the worst by those who hated its precursor episode "Demon" and didn't like revisiting the concepts.
The entire show, really. Many Trekkies like it, thinking that it's cool, funny, and action-packed. Others loathe the shaky writing, weak characterization, Neelix, and multiple cases of They Wasted a Perfectly Good Plot. The numbers are about 50-50, and depend a lot on age (those who watched VOY growing up tend to like it more, just as those who were raised on TNG give its infamous first season a pass). The weak writing exacerbated matters, as contradictions abound—and Trekkies, a notoriously detail-obsessed fandom, will always pick over every last detail in an argument, no matter how small. In general, pickier fans rate Voyager lower than less-picky fans, although this is by no means universal.
"Scorpion". Fans of Janeway claim that she was defending the galaxy from a threat greater than the Borg. Anti-fans claim that she was using the equivalent of bioweapons against the only species able to easily defeat the Borg on the basis of limited information. The latter often point to the later episode "In the Flesh" to show that Species 8472 is nowhere near as evil as the Borg.
There's a split between fans who consider Seasons 1-3 to be better, and those who prefer Season 4-7. Those in the former group claim that whatever their quality, the earlier seasons at least tried to stay true to Gene Roddenberry's vision, and that the latter seasons betrayed said vision by instead going for the Darker and Edgier, more action-oriented style that DS9 and Star Trek: First Contact employed. On the other hand, those who prefer the newer seasons tend to point out that the show was in serious danger of cancellation by the end of Season 3, and that the Re Tool for Season 4 ensured that the show got to the full seven-season run that the two previous Trek shows did.
Contested Sequel: Just scan this page. TAS, TNG and DS9 don't take anywhere near this much flak; the only TV show entry that does is Enterprise.
Designated Hero: Some of Janeway's actions (allying with the enemy of all sapient life in "Scorpion", hypocritical actions against Ransom in "Equinox", and murder in "Tuvix" just to start) seem grossly immoral to some fans, to the point where they might be considered a Moral Event Horizon if Janeway wasn't The Captain and protagonist. The Status Quo Is God format of the series meant that especially questionable actions (such as separating Tuvix against his wishes) were rarely or never brought up again. She did get the occasional What the Hell, Hero? (usually from Chakotay) but again, status quo dictated that they end their disagreement by the end of the episode.
Designated Villain: Species 8472. Their initial appearance has Janeway decide to ally with the Borg to destroy them because... one Species 8472 soldier shot a warning shot off Voyager's bow, and Kes (a telepath with powers that are repeatedly unreliable and unstable) says that they're very angry and shouting xenophobic war cries telepathically.
Die for Our Ship: In romance fanfics, Chakotay or Seven is generally on the receiving end of this by J/C or J/7 shippers.
Ethnic Scrappy: Chakotay is sometimes seen like this. Despite being in a role of authority and a chief officer of Voyager, he's seen as a mishmash of all the worst traits of white people writing about Native Americans, including his mystical insight powers and tracking and survival mastery. Not helping the character is the background materials. All of Chakotay's backstory was Based on a Great Big Lie provided to the Voyager writers by an Native American expert "Jamake Highwater", who later was revealed to be a fraud and had absolutely no Native American heritage whatsoever, and whose only knowledge of Native Americans came from Hollywood. The absolute worst part of this is that Robert Beltran, who is second-generation Mexican-American with a lot of Native American roots, ended up utterly furious at the portrayal he was being asked to perform, and has gone on to openly denounce his role in the show and break with a lot of the former crew (though he has a bit more sympathy for his castmates).
Taken Up to Eleven in "Tattoo", an episode where Chakotay finds out that his ancestors were half-animal savages before magic space white men taught them how to be human.
Expectation Lowerer: Ensign Harry Kim. Easily the least useful person aboard the ship. Even Neelix can lay claim to motivating the crew to do their best, or wheezing out a campfire song from time to time. Harry can't even get laid on the holodeck — that's how socially repressed he is. One tryst with a TOS-style space babe left him with a venereal disease... and Janeway wouldn't let him hear the end of it ("I wanted to leave a lasting impression"). Oddly considering his manic desperation to get back to Earth, it is Harry who is assigned to the ship in "Future's End" whilst the others get to romp around in L.A. (And Harry Kim in command of Voyager is every bit as thrilling as you imagine.) He never wins one single Kal-toh game against Tuvok in their seven-year voyage, and Icheb only wins by disregarded Harry's seasoned 'advice'. After a while you begin to wonder if the show runners have it out for Garrett Wang.
The show runners intended to kill him off in "Scorpion", and was only saved by Garrett Wang making the People Magazine list of "50 Most Beautiful People in the World".
This got even worse when it was revealed that Wang was the only actor in the entire franchise who ever had their request to direct an episode be refused by the producers. By this point he'd become so clearly constantly mistreated that some fans started accusing Rick Berman of having something against Asians.
At one point in "The Omega Directive", Seven solves a puzzle game that Harry is playing in about two seconds. Yes, she's a superintelligent Borg... but Harry's supposed to be an educated bridge officer! Even for Harry Kim this incident is pathetic.
Family-Unfriendly Aesop: "Mortal Coil" gives us the message that there is no afterlife, you won't see your dead loved ones again and that the only way to find any meaning in all of existence is in others. The fact that the scenes used to hammer this in consist of Naomi's adorable antics make it even worse. According to Memory Alpha, Bryan Fuller's own disillusionment with Catholicism was the catalyst for the Cessation of Existence message in "Mortal Coil." Add the fact that this episode originally aired one week before Christmas on to that. Given that the episode takes place during a Talaxian holiday celebrating family and kinship, the air date was probably intentional. Barge of the Dead becomes something of an Author's Saving Throw which allows both views of atheists as well as those who believe in an afterlife to coexist on the show.
Janeway and Chakotay. People who prefer this pairing (which evidently included the Star Trek: Voyager Relaunch writers) tend to assume that Chakotay and Seven were just a brief fling, and that he and Janeway hooked up permanently after returning to Earth.
Seven and the Captain is also vastly preferred over Seven and Chakotay. For that matter, you can probably find more fans of almost any pairing than that one, even Tuvok/Neelix.
Since Naomi ages so fast, many fan-fics set when Naomi is older pair her and Icheb up.
Fanon Discontinuity: There are a number of very silly Idiot Plots, in the first two to three seasons in particular, that are written out of fan consciousness for the sake of mercy.
Remember "Threshold", the episode where Tom Paris made it to Warp 10? The fans decided not to. In fact, even the series itself struck it off.
"Twisted" wasn't even well liked by the actors - in particular, it's Robert Picardo's least favorite episode.
Gotta Ship Em All: Due to the fact that the crew is trapped on the other side of the galaxy with decades between them and home, the various members of the crew get shipped with everybody else on the ship (pun unavoidable). This includes Naomi Wildman, who by rights probably shouldn't be shipped.
And yet somehow, no one (at least on the Internet) appears to have shipped Seven of Nine and Ensign Wildman until 2015. Considering how many ships there are for characters who didn't even appear in the same series (Janeway/Dr. Crusher being a fairly common one), Seven and Samantha having shared at least one scene (Mortal Coil), AND Seven's friendship with Naomi, this seems like a natural fit.
Season 3 is commonly felt to be at least a little better than the first two seasons, with the "Future's End" two-parter in particular being considered to be where the show's overall quality started to drastically improve (in no small part due to the Doctor getting his mobile emitter). Seasons 4—7 are widely regarded as a major improvement.
In particular 4—7 showcased greater consistency in Janeway's character and decreased the Omnicidal Trigger Happy aspects of her personality a fair bit. The story plots also became less stupid, to some degree, and Seven of Nine became a regular character as well (this coincided with less screentime for characters like Chakotay which really didn't hurt at all).
In addition, those less popular characters like Chakotay, Harry Kim and Neelix had the traits that people found annoying toned down. Chakotay's Magical Native American mysticism faded away and he acted more normal (with a couple of exceptions, like the lucid-dream episode); Harry became less of a "dweeb" and started to stand up to Tom more, and earned command of night shifts; and Neelix's obnoxious traits were somewhat reduced as he took up the kindness and responsibilities of being a morale officer (this due largely to breaking up with Kes in Season 3, and later Kes leaving the ship, so he couldn't remain so jealous of her). It also helped that Neelix got less screen time and at one point even recognized how annoying he was in "Once Upon A Time"—ironically an episode where Neelix was being relatively innocuous.
Also, the Kazon stopped showing up after season 3 (except in flashbacks or as holograms) and were replaced by worthier opponents like the Hirogen and Borg.
At one point, Neelix is forced to get makeup and surgery so that he looks like the Grand Nagus of the Ferengi ("False Profit"). His actor, Ethan Philips, would later go on to be one of the Ferengi seen in the Star Trek: Enterprise episode "Acquisition". He previously played a Ferengi in "Menage a Troi" in TNG, so this may have possibly be an in-joke.
One for the episode "Scientific Method." Try not to laugh at how Chakotay looks when he ages; his face is elderly, but from the neck down he's still oddly buff for such an old man. Fast-forward ten years, and watch Robert Beltran in interviews or con panels. His hair is silver, his face is wrinkled, and he still looks like he could kill you with one punch. Guess his appearance in "Scientific Method" wasn't so far-fetched after all!
In "The Voyager Conspiracy", Seven Of Nine develops symptoms similar to paranoid schizophrenia due to information overload and starts linking several unrelated events as "proof" that Voyager is actually part of a Federation plot to capture her. In 2011, a group of neurobiologists who believe schizophrenia might be caused by a lack of information filtering in the brain have tested their theory by overloading an A.I. with information, which then proceeded to spout off pretty schizophrenic like statements, including taking responsibility for a terrorist bombing.
In "Virtuoso", the Doctor finds himself as a worshipped musical performer by an entire planet that had never heard music before and is ready to leave Voyager to become their biggest celebrity... until the race in question programs their own singing computer program that can surpass the human vocal range, making the Doctor obsolete. Speaking of a computer program that can sing beyond the human vocal range...
The in-universe holonovel is also hilarious in that it is little more than a slight exaggeration of the way the EMH was actually treated at multiple points in the show; Jenkins's lack of care for the novel EMH is eerily similar to Janeway's disregard for the show's EMH in "Latent Image", the portrayals of Paris and Torres make a lot more sense when you remember that Torres turned the EMH's fictional family into a dysfunctional wreck in "Real Life", and then Paris told the EMH that he should watch his holo-daughter die.
In "Dark Frontier", when Magnus tells a young Annika (in the flashback scene) to put down the Borg cube model, he tells her it's "not a toy"- it actually is a toy, the Borg cube made by Playmates.
Captain Braxton's defining line "A leads to B, and B leads to C" will never sound the same again in a post-Human Centipede world. Made worse/funnier by the fact that Braxton is, in a way, a mad scientist.
In "Worst Case Scenario" (written by Kenneth Biller), Torres bothers Paris about injecting some romance into the holo-novel. When Biller became executive producer and showrunner in Season 7, Paris and Torres moved past the occasional Ship Tease and got married.
In the Season 2 episode "Maneuvers," the Kazon torture Chakotay by punching and beating him, and are frustrated when he refuses to talk. Come Season 5's "The Fight," we learn that getting punched is Chakotay's favorite hobby. No wonder he was laughing at Culla during that interrogation.
During "Favorite Son", the Nasari's ship name is the Nerada.
"Holy Shit!" Quotient: While "Coda" had some definite problems, the scene where the Doctor euthanizes the Phage-infected Janeway is downright chilling. Also, the scene shortly thereafter where Chakotay tries and fails to bring Janeway back with CPR; this doubles as a Tear Jerker.
The introduction of Species 8472, easily overwhelming the Borg, is one of the best teasers in the entire show.
Depending on your interpretation, there's a lot of this between Harry and Tom. Particularly in "Demons", where they are the first of the Silver Blood duplicates to exist, essentially making them Adam and Eve. Yeah...
"Non Sequitor". Harry gives up his hot, horny fiance and successful job to try a suicidal plan to be back with Tom Paris again.
Chakotay/Paris also has a sizable following. It's surprisingly easy to read their tension and Tom's protectiveness of Chakotay as the result of their being bitter ex-boyfriends who still have feelings for each other.
Janeway/Seven, to the point where Seven was reattaching one of Janeway's rank pips while Janeway was asking if she'd ever considered trying romance.
Any time Tuvok mind-melds with another man (see "Meld" and "Random Thoughts") the whole thing is replete with Homoerotic Subtext.
Inferred Holocaust: Inverted with "Dragon's Teeth". The bad guys escape to menace the Delta Quadrant... But yet, there were only 600 of them, many of whom obviously died in the preceding battle. Gedrin's attitude indicates there may be strife with within what little is left of them, but even failing that, their technology is so out of date that it takes 10's of their ships just to threaten ONE modern vessel. Further reinforced by the fact that some of them get trapped in a void later on.
If anyone asks, you like (or dislike) Kes and Seven equally. Because otherwise a horde of fans will tear you limb from limb.
And don't, whatever you do, say you like the show (or like most of it minus the ridiculously stupid episodes that are Fanon Discontinuity). Just... don't.
Don't say that you dislike the show or criticize any of the characters, either. You will get death threats for criticizing Janeway on Tumblr.
Any criticism of Janeway invites immediate claims of sexism.
To this day, the fandom still argues whether Janeway blowing up the Array was the right call because even a short-lived species deserves to live, or a boneheaded move that stranded her crew for no good reason. Even close analysis of the script is somewhat ambiguous, thanks to late rewrites by Jeri Taylor that muddled the issue from what seems to be simple pragmatism (the script indicates that despite sending Tuvok to figure out its workings, Janeway is physiologically incapable of operating the array) to unusually-justified moral grounds (Janeway's actual reasoning for blowing up the damaged, already likely unusable array is to protect the Ocampa, which is not only a technical violation of the Prime Directive that Janeway claims to hold sacrosanct but also sort of pointless as due to their screwy biology the Ocampa will go extinct within a couple of centuries at the absolute most).
This is inflamed by the fact that Chakotay and Seven's romance was shoehorned in very late in the series, after they had spent the better part of four seasons barely interacting, whereas several of Jeri Taylor's early-season episodes (notably "Resolutions" and "Coda") were set up as blatant Janeway/Chakotay romance stories.
In fact, best to stay out of the shipping community entirely; besides Torres and Paris's generally well-handled relationship, which even anti-fans tend to agree was a highlight of the show, the flame wars between J/C, C/7, J/7, Doctor/7, Harry/Tom and even Torres/Seven can be epic in scope.
Launcher of a Thousand Ships: Due to how close the crew wound up becoming with each other, there are multiple fics for virtually every pair imaginable, almost all of them pretty justifiable. However, honorable mention must go to Janeway, Seven, and Tom Paris, who get the most action in the fan fiction. (Janeway, because being the captain, she had a close relationship with each senior officer; Tom, by being the guy who tried to befriend everyone; and Seven, for obvious reasons.
LGBT Fanbase: Lesbians. Love. Janeway. Quite a few of Star Trek's queer fans grew up idolizing Janeway, and of course, her and Seven are a popular ship. It seems only fitting that Kate Mulgrew would wind up on Orange Is the New Black, another show with a rabid LGBT following.
Magnificent Bastard: Seska disguises herself as a Bajoran, infiltrates the Maquis, is communicating with and slipping tech and information to the Kazon during most of her time serving with Voyager, isn't found out for a least a year, engineers a cover up that's almost successful, when she is discovered she had already planned out and executes an escape, forges an alliance with the Kazon-Nistrum, has the faction leader Culluh basically as her puppet right from the start, is directly responsible for most of the Nistrum's victories, including the successful capture of Voyager at the end of season 2, and even after she dies she possessed the forethought to set a trap in one of the holodeck programs at some point during her possession of Voyager in an attempt to kill several members of the crew in the event they retook the ship that she put in just in case. In fact, over the entirety of the Voyager Seska is one of the very few truly cunning villains in the series to last more than an episode or 2.
The aliens in "Scientific Method" come across as an entire civilization who crossed the Moral Event Horizon long ago and have just kept on going. They routinely do medical experiments on sentient creatures, mutilating, torturing them, and even killing them if they feel it will benefit their medical research to do so. They feel completely justified in their actions and not only do they feel no remorse or regret over their actions, they feel that what they do is noble and beneficial. Genetically deforming, maiming and killing the crew of Voyager is the Nightmare Fuel evidence of their crimes and that is only the tip of the iceberg. What is really terrifying is that their flimsy justifications allow them to murder entire societies with impunity and go on torturing and killing as many sentient creatures as they feel is necessary for their "research."
Janeway allies with the implacable enemy of all sapient life in "Scorpion", which many viewers consider to be an unforgivable crime. She actually gets called out on this later on by an alien whose species was assimilated because of her actions.
The part in Flesh And Blood where Janeway notes that the holodeck technology wasn't given to the Hirogen for them to get themselves killed. While she clearly wasn't suggesting that this was their actual goal, the implication was still quite funny.
"Meld" has a seriously epic Take That, Scrappy! moment where Tuvok strangles Holodeck!Neelix. Except the way Holodeck!Neelix's body collapses, with the weird head-tilt, isn't so much "corpse" as it is "say whaaaaat?"
Never Live It Down: Fans who don't like Janeway often point to "Tuvix" as a justification, where she beams a sentient being out of existence because the process would revive two of her friends, effectively taking one life to save two. This decision (which is, unquestionably, one of the most brutal scenes in the whole franchise) is a heated subject of debate even today.
The possibility that the "loved ones" you see during an Near-Death Experience are actually beings who want to devour your soul. As if this weren't horrible enough, it could also mean that many religions are essentially massive farming operations, as people conditioned to unquestioningly trust certain religious figures would be likely to follow them into the light without a second thought.
Well, we also know now that the Klingon religion is true, or at least can be manifested—although that in itself might be a cause for Paranoia Fuel—which indicates that other religions are true as well. We also have verification that spirituality and unknown planes of existence exists as well, courtesy of "Sacred Ground", and that belief and faith do in fact have an impact on the real world. Now that is both awesome and insanely confusing, and now we can be absolutely sure that someone is out there watching the confusion and laughing their head off. Not that Q wasn't doing a wonderful job already...
Although the existence of Klingon Hell seems (to some viewers) to be ambiguous, not really saying one way or another if Torres was actually in hell, or simply hallucinating due to the concussion.
The writers seemed to forget that Kes dumping Neelix in "Warlord" wasn't real, since she was being possessed. Afterwards they're presented as broken up for real, with no further explanation. A scene was filmed for the episode "Fair Trade" to give some closure to the relationship, but it was cut due to time constraints.
"Resolutions" was meant to resolve the whole J/C issue. But as their Ship Tease continued throughout the series, the audience could have been forgiven for expecting they'd eventually hook up.
The Scrappy: The entire Kazon species basically constituted one of these on the first two seasons of Star Trek: Voyager; in spite of the fact that the entire species seemed to be rock-stupid and technologically backwards, Voyager somehow managed not only to keep running into them, but to keep running into the same ones. Later in the series, the writers themselves took shots at the Kazon by revealing that the Borg took a pass on assimilating them on the grounds that doing so would undermine their perfection. Their role as a major power in the Delta quadrant seems an Ass Pull as well. On the first episode they are shown, they are depicted as a small nomadic slave-trading tribe always on the move to find vital water supplies... but the minute Neelix pisses them off, out comes the armada of Voyager-level warships always on the Voyager's tail. It's almost like refusing change to a bum on the subway only to find you pissed off Don Corleone.
While this example by no means detracts from the beauty of it. Word of God states that in the last shot of the opening sequence (done in CGI), the three (incredibly tiny, almost window-like) grey patches on the bottom of the Voyager's nose before it jumps into warp were actually missing texture spaces. This is the shot in question◊
"Threshold" is generally considered as the worst episode in this series. The effects certainly don't help.
The lightning/plasma disc/plate on the Borg alcove, essential component of Borg technology related to the Borg's regeneration cycle and connection to the Borg hive mind, or cheap novelty item for your home?
Strangled by the Red String: Seven of Nine/Chakotay. After three and a half seasons of them having only a professional relationship and almost no interaction outside of business, Seven suddenly develops an unrequited attraction to Chakotay in the second half of the final season.
A great many episodes have situations in which they have an opportunity to do something that would be very advantageous for the crew, only to have Captain Janeway refuse for reasons typically related to the Prime Directive. Some character inevitably complains about her decision and points out that her moral arguments for why they can't take advantage of the opportunity don't actually make any sense, but they're always portrayed as being wrong, while Janeway is right.
In the pilot episode, we're supposed to see Janeway's decision to destroy the Array that brought them to the Delta Quadrant in order to protect the Ocampa, rather than using it to get home, as a noble choice. However, Tuvok pointed out that destroying the Array would not only leave them stranded but could be considered a violation of the Prime Directive because it would affect the balance of power in that sector. He's waved off with a one sentence bit of "wisdom" from Janeway about how they're already involved so the Prime Directive no longer applies. When B'lanna also objects, she's told to shut up because Janeway is the captain. What's frustrating is that they undermined the whole dilemma by having Tuvok mention that the Array would take several hours to use without the Caretaker's help and that was before a Kazon ship crashed into it, disabling the self-destruct and God knows how many other systems, so they probably couldn't use it in the time they had.
Shortly before she defects to the Kazon in the first season, Seska delivers a "The Reason You Suck" Speech to Janeway. While the episode tries to make her out as being a raving lunatic, it's hard not to agree with some (if not all) of Seska's criticisms... the only problem is that she wants to barter technology with the Kazon. Forgetting all ethical arguments, these people killed themselves with a replicator. Plus, Voyager with all its technology is a force to be reckoned with. Giving away its technology (which could be sold off and/or duplicated) would dilute its strategic advantage as a highly-advanced Starfleet ship.
A variation: in "Gravity" the audience is supposed to agree with Tom Paris that the human way of being in touch with our emotions and having them in our lives is the right way, in contrary opposition to the Vulcan master who taught Tuvok to suppress his emotions. Paris has a real problem with accepting that Vulcans aren't humans. Vulcan emotions are far more volatile, erratic and all-consuming than humans' (whose emotions are less violent), and for a Vulcan being in love can be legitimately destructive, and not in the metaphoric sense that humans use.note They're not just assuming that their emotions are stronger; remember that Vulcans have mind-melded with humans, putting them in a position to compare their emotions Not to mention that other episodes of this show have Tuvok fully justify his emotional repression by demonstrating to people what it looks like when he lets it go. (This is a fairly common writing mistake with Vulcans in general: they're frequently portrayed as being just super-stuck up, repressed humans rather than The Fettered.)
Stoic Woobie: Seven. As good as she is at keeping her emotions in check, you know when she starts getting just slightly teary-eyed or starts acting even somewhat angry, she's really feeling it.
In "The Thaw", the crew are in the middle of a difficult debate on the nature of fear, trying to find a way to deal with a Monster Clown that has taken over a Lotus-Eater Machine and is capable of physically scaring the inhabitants to death. Neelix suggests telling jokes to overcome the Monster Clown, under the reasoning that laughter overcomes fear. The rest of the crew just stare at him with a collective look of irritated disgust as he splutters out mid-sentence, realising how badly his idea is going over with everyone. Unfortunately for the audience, not only doesn't this happen every time Neelix's opens his mouth, but it's actually one of his better ideas and at least has some degree of logic to it.
In "Meld", Tuvok fears he is losing his self-control after a mind-meld with a psychopath. He decides to test the limits of his self-control by exposing himself to the circumstances that he thinks are most likely to make him snap by simulating them on the holodeck. His choice? Having to share a room with Neelix at his most obnoxious. Needless to say, he discovers what his limit is.
In "Rise," Tuvok chastises Neelix for wasting time in idle conversation when they're under serious pressure to repair an orbital tether so they can escape a disaster. The Aesop of the episode is that Tuvok needs to lighten up and be friendlier to his coworkers, but it's pretty hard to see the situation they're in and not think, "Seriously, Neelix, just shut up and do your job for once."
The aforementioned line about the Borg refusing to assimilate the Kazon because they had no useful characteristics at all.
Neelix suffers Eye Scream in "Tattoo", the only amusing part of an otherwise interminable and racist episode.
Just watch an episode with the crew behaving out of character ("Meld", "Remember", "Night", "Nemesis", "Timeless", "Memorial", and particularly "Workforce") to see how wasted their talents were on most weeks.
Seska could have been a very interesting cast member, offering morally ambiguous solutions and a point of conflict for both the Maquis and Starfleet crew if they'd let her stay—after all, she'd want to get home too—especially if/when they learned about the Dominion War and what that did to Cardassia. Instead, they made her a mustache-twirling villain (figuratively, of course) who decided to throw her lot in with a misogynistic society of rock-stupid gangbangers that couldn't even figure out how to use a replicator.
Most of Kes's episodes revolved around her latent powers. Which was cool and all, but the concept of the Ocampa species is basically an inversion of the Trill and Dax from DS9. Sure, it's wobbly science, but only a few of her episodes explored what it would be like for a person who has less than a decade to experience the universe.
This show had a horrible habit of introducing potentially interesting recurring characters and then either getting rid of them only a couple of episodes later or just never using them again. Carey mostly disappeared after the first season, Hogan was unceremoniously killed, Jonas was killed instead of imprisoned (where he could have made a good recurring anti-villain) and they phased out Wildman and Vorik for no reason. Interesting characters like Dalby, Chell, Suder, Lessing, Ceres, etc. were never used again after their introduction (with the exception of Chell, once, several years later, and not to the best effect; and Suder who was killed in his second appearance).
Garrett Wang openly complained about Harry Kim's utter lack of character development and being constantly written as the Ensign Newbie right up to the end of the series seven years into the journey. The Star Trek: Voyager Relaunch series and Star Trek Online rapidly moved to fix this, starting with jumping him two grades to lieutenant, and ending with him in command of the USS Rhode Island in STO's Delta Rising expansion (as he had in the alternate future in "Endgame").
Neelix, actually. He has a Dark and Troubled Past where he lost his family in a war where he dodged the draft because he was afraid to die, and then had to spend years trying to survive in a hostile region any way he could. His initial purpose is to be the crew's guide, but the ship eventually passes beyond the regions he's familiar with—leaving him questioning his purpose and where to go from there. That had the makings of a character with pathos and complexity. Instead, we got a pompous, comic relief goofball who spent the first couple of seasons with a creepy jealous streak, and barely got any Character Development outside of what was just mentioned.
Subverted with (surprise, surprise) Seven of Nine. Jeri Ryan is on record as having been worried, when she accepted the part, that her character would get very rushed Character Development and then simply turn into the ship's Girl of the Week. The first did not happen; while the second arguably did, they at least managed to save it for the final season.
Janeway herself. Her characterization is infamously inconsistent to the point that Kate Mulgrew actually posited that Janeway was mentally ill. Meanwhile, Mulgrew's acting is actually one of the strongest elements of the show; it's not unreasonable to state that a more consistently-written Janeway would've removed most if not all of the Broken Base moments in the show's run.
Chakotay. A badass rebel leader with a Native American past? Just make sure that you don't portray him as a racist stereotype and have him consistently serve as a foil to the straight-laced Janeway, he'd be essentially a Spear Counterpart to Kira Nerys in a situation much better suited to rebel-leader skills. Instead, Chakotay's role mostly consists of nodding when Mulgrew says an important line, acting out racist stereotypes of amalgamated Native American spirituality, and looking stern. No wonder actor Robert Beltran openly dissed Voyager in interviews.
What strikes immediately about "Caretaker" is the amount of promise it shows. You’ve got a well-cast female captain, a crew consisting of outlaws, misfits, refugees, a grouchy holographic Doctor, and a ship which is lost and alone in an uncharted area of space. Surely this is going to be an exciting return to the days of TOS? "Caretaker" boasts a huge budget for the time and sets up its characters and the series ethos with aplomb. But apparently the fellows in Paramount and UPN's marketing department had other ideas... While the series had numerous moments of greatness, it was ultimately a frustrating and unsatisfying experience for nearly everyone involved.
This is especially evident in the episode numbering scheme- originally, the show didn't start at 101, as a show should normally start at, but at 801... as in "We're trying to be the eighth season of TNG." Economics kill a lot of shows after actors finish their original contract and get a big raise to do one or two final seasons. If it weren't for Paramount's long-sought goal to have its own TV network spearheaded with a new Star Trek show, the best course would have been for TNG to continue indefinitely in syndication, gradually replacing its cast like ER or other very long-running shows have done. It would have seemed perfectly natural for senior Enterprise-D crew members to move on with their careers and new ones to come aboard.
According to some of Voyager's production staff (including the late Michael Piller), Voyager was a victim of Executive Meddling. UPN execs wanted TNG-type ratings, and they decided the best way to achieve that was to turn Voyager into TNG-Lite. The result: little or no character conflict, no ongoing story arcs (for example, producer Brannon Braga and his best friend Ron D. Moore wanted the beloved "Year of Hell" two-parter to be an entire season, but were vetoed by UPN), and various other flaws (real and imagined) the series had. "The Void", an episode which aired a stone's throw away from the series finale, is a glimpse of what VOY might have been.
Kes and Neelix had a breakup during season 3 that didn't really get so much as lip service after it started in "Warlord" (3x10); it just ended somewhere between two episodes (3x17 and 3x18). Ethan Phillips (Neelix's actor) found this a frustrating point (after all, the relationship had featured prominently since the first episode)—and to make matters worse, they actually filmed a scene for "Fair Trade" (3x13) that decisively gave it finality, but it got deleted from the final cut.
The production issues even showed themselves in the episodes, with Mulgrew struggling to figure out Janeway's character, Beltran's actor revolt against the role and Garrett Wang getting direction to be constantly expressing Dull Surprise, amongst other problems.
The episode "Worst Case Scenario" has an excellent plot hook: Torres (a former Maquis) finds a holodeck program hidden away in the computer which depicts a Maquis revolt on Voyager. It's later revealed that it was designed by Tuvok as a way to train security to handle such a scenario. The episode completely fails to do ANYTHING interesting with this, possible because the character (by that point) didn't have the depth to make the episode interesting. SF Debris also noted on this one how sad it was that by this point, the supposed major hook of the show in having Starfleet and Maquis forced to work together had become such a non-issue that Tuvok literally had to write his own fanfiction for it to be explored at all.
The episode "The 37's" involves the crew finding the frozen bodies of Amelia Earhart and several other humans from 20th Century Earth. After the 37's are revived, they don't do anything. One of the most famous aviators in history is a character on Star Trek, and she takes up space. There could have been an interesting story about the mysterious aliens who kidnapped people from the other side of the galaxy, but we don't get that either.
The Agony Booth, in a review of the infamous "Threshold," points to the episode that aired a week prior to it as the death knell of the Star Trek franchise. In "Alliances," Janeway considers teaming up with one of the Delta Quadrant's factions against the predatory Kazon, potentially changing the direction of Voyager from "find a possible way home that disappears at the end of the episode" to a story about creating an improvised Federation on the frontier. Instead their new allies backstab them and Janeway dissolves the alliance, then delivers a speech about sticking to Starfleet principles and avoiding diplomatic entanglements. Or in other words:
Dr. Winston O'Boogie: But if there's one good thing I can say about Voyager, it's that it reached such a predictable level of sameness, that it became like comfort food television. Just like ordering a Big Mac, you always knew what you would see when you opened that box. Unfortunately, this is only good for certain situations, like when you have an hour to kill and don't want to think too hard. For a series, it was ratings death. There was zero chance the show would ever get any critical notice, or become water cooler talk.
"Fair Trade" was the first episode in a while to show Neelix outside his comfort zone. He faced the end of his usefulness as a guide, as the ship was moving into a region of space he was unfamiliar with. To maintain his usefulness, he proceeded to do one questionable thing after another and agonize over the guilt. The episode ends with him accepting responsibility for his actions, but rather than be a turning point and examine different ways he could contribute, succeeding episodes continued to portray him as a comedic goofball.
The "Basics" two-parter was a pretty formulaic outing, but it represented potential for future stories: Seska being taken prisoner, Suder struggling with having killed again, and the matter of Chakotay's son with Seska. Instead, what we got was Seska and Suder killed off rather anticlimactically, while the baby is retconned as not being Chakotay's at all (despite it being the entire reason this whole two-parter happened in the first place). Writer Michael Piller was severely disappointed with this—noting that Executive Meddling was responsible for each development. Coincidentally or not, Piller stepped down as executive producer not long after this.
"The Swarm" ends with the Doctor having to be rebooted with a reinforced system after all the forming of his own personality is causing his program to break down. This appears to have erased all the character development he'd gone through, but then he starts singing opera as he gets back to work. Robert Picardo was quite disappointed that he was completely back to normal by the next episode, rather than getting a whole arc about regaining his personality.
Too Cool to Live: One, from "Drone". A Borg drone comprised of technology from a few centuries in the future, and whose humanity had nurtured since his "birth". Unfortunately, that advanced technology also quickly made him a priority target for the Borg, and he allows himself to die to prevent the Borg from relentlessly pursuing Voyager just to assimilate him.
The Untwist: "Scorpion" treats the fact that the Borg were the aggressors in the conflict with Species 8472 as a major revelation. Considering the mission statement and track record of the Borg, that should've been the default assumption.
The Borg Transwarp Hub seen in the series finale is quite impressive.
"Unimatrix Zero", despite not exactly being one of the most well-liked episodes, at least opens with a really nice shot of eye candy, and the Borg costumes for Janeway, Torres, and Tuvok deserved more screen time.
The Woobie: Most, if not all, of the characters have Woobie moments.
Harry, the young naive "dweeb," who gets killed, tortured, diseased, etc. probably more than any other character.
Seven gets a lot of Woobie episodes, with her traumatizing past.
The look on Chakotay's face every time he realizes that he's been back-stabbed by a woman or mind-raped by aliens AGAIN, is heartbreaking. The famously funny line "Was there anyone on that ship who was working for me?" was clearly not intended to be funny, but rather to verbalize his frustration at his own failures as a leader.
Torres, when she finds out that the Maquis were all slaughtered by the Dominion. She even goes so far as to run dangerous scenarios in the holo-deck with no safety on, the 24th Century equivalent of self-harming herself (or at least risking self-harm) over the guilt she feels at surviving.
As if B'Elanna's life wasn't sad enough, the universe seems to personally have it in for her: she is killed in two alternate futures ("Before and After" and "Fury"), and her duplicate is the first to die in "Course Oblivion."
The Silver Blood duplicates of the crew, particularly Harry Kim. One of the few genuinely heartbreaking Voyager moments that doesn't involve the EMH or Seven is Harry Kim's duplicate, sitting on the bridge, desperately hoping for salvation as he dies, and failing himself, his ship, and his crew as he dies an ignoble death that ends up as little more than a note on Janeway's log. Most viewers, fans and anti-fans alike, will freely admit to tearing up during this scene.
On the surface, Neelix is nothing more than an arrogant lying incompetent asshole, and most fans hate him, feeling that he was little more than a prototype of Jar-Jar Binks. However, while his species was xenophobic, arrogant, and generally incompetent to begin with, many of his kind were killed when his home colony was vaporized in a violent war with another race—made worse by the fact he was a cowardly war deserter that suffered survivor's guilt because he only survived due to having run off to another planet. His time as a junk scavenger placed him under the watch of the Kazon, and the woman he loved was not only abused by the Kazon but only had a life span of 9 years. Try as he might to help the crew in their situation he often annoyed them. He lost his lungs to the Vidiians and had to receive an emergency transplant from Kes just to survive. At one point a transporter accident bonds him and Tuvok into one being (with "Tuvix" being a bad example—he had to be "killed" just to save the two that made him). Kes eventually broke up with him due to his abusive and hyper-jealous treatment of her, and Neelix was consistently stuck inflicting his incompetence on Tuvok, which eventually caused him to snap and chew out Tuvok—Tuvok did learn to be a bit more tolerant of Neelix's persistent incompetence, though. Then as Voyager moves out of the area of space he knows he finds himself feeling even more useless and commits a criminal act hoping to get a useful map. On one mission he is killed, his only salvation being Borg nanoprobes that revive him but sends him into a temporary depression, believing that he is merely a reanimated corpse and that the "real" Neelix died. Dealing with the possibility that Samantha Wildman may die led to extreme troubles in dealing with Naomi Wildman. The series didn't really let up on treating him like a punching bag until his final episode in which he meets a colony of Talaxian refugees and stays with them shortly before Voyager returns home.
Kes. Abused by the Kazon, then "rescued" by her abusive boyfriend who become homicidally jealous when Kes dares to spend time platonically with another man something like a month after she said that she wanted to have his baby one the one occasion in her entire life that she would be able to do so. Also, she will grow old and die before all of her friends have even aged a decade.
"Hunters" is a massive Woobie episode for virtually all of the major characters, as they get letters from home, some containing heartwarming news, and others heartbreaking.
Even some of the show's actors might qualify.
Robert Beltran (Chakotay) has a negative reputation among some fans, for his problems with the show's writers and some instances of unfriendly behavior at cons; but he has cause to be upset. He was forced by contract to play a character that turned out to be a racial stereotype; he had only signed on to work with Janeway's original actress, Genevieve Bujold, but was stuck when she was replaced by Kate Mulgrew. His performances in later episodes range from wooden to openly expressing his loathing of his part in his tone. He becomes even more sympathetic when one reads up on the actor; he grew up "low income" with a brother who had Down Syndrome, and as a result now does charity work for low-income kids and the disabled. It's easy to see why he doesn't think the writers of Star Trek or their middle-class fans deserve his sympathy (not that this is an excuse for unprofessional behavior, but it does make his actions understandable).
Ethan Phillips. My god, the man tries so hard. He's a good actor, too—his work on "Benson" isn't half bad. But Neelix is consistently written as a lying, incompetent braggart who refuses to do the job that he gave himself and gets people killed through his own incompetence while saying schmaltzy lines. On top of that, Phillips had to be in the studio extra early in order to be covered up with makeup that made him look like a hedgehog on drugs, and some fans take their undying hatred for his character over onto the actor. (Mulgrew and Beltran suffer from this to a lesser extent)
Garret Wang, Harry Kim's actor, who loves Trek and is generally a nice guy in Real Life, but was constantly screwed over by the writers.