Star Trek: Voyager/WMG

Janeway was Kicked Upstairs prior to Star Trek Nemesis

 * 1) While the Alternate Timeline in "Endgame" forced Janeway to endure the things that earned her the title of Admiral Badass upon returning home, she never did get that chance in the main timeline. With a record of questionable decisions, now without years of strife to make amends, Starfleet made Janeway an Admiral to keep her away from the front lines where she'd screw up the worst.
 * Now we know how there got to be so many Insane Admirals in Starfleet.
 * Considering she crippled (or destroyed) the Borg, Saved and bolstered relations with the Q, and the Federation was captivated by Voyagers story I always thought it was more of a publicity stunt.
 * To fans who are annoyed that Janeway got a promotion "over" Picard, keep this in mind: Picard was *offered* promotions before, but rejected them, because he *wants* to continue to captain the Enterprise and stay with his crew. Janeway, though she undoubtedly loves her ship and crew just as much, has spent seven years lost in space, with no connections to Earth or her family. She probably accepted a promotion gladly, because she was tired and needed to be back on Earth at home. (This does not discredit the hilarious "Kicked Upstairs" theory however. Merely suggesting that Janeway was well aware that she was being "kicked upstairs," and more than fine with it, because *she* didn't want herself on a starship anymore either!)

Voyager is responsible for the Obama presidency

 * 1) Jeri Ryan wanted to move to Los Angeles after she got the job as Seven of Nine, but her husband at the time, Illinois politician Jack Ryan, objected.
 * 2) A bitter divorce drama plays out in 1999, where the results are sealed in the interests of their child.
 * 3) In 2004, Mr. Ryan campaigns to be the Republican nominee for the U.S. Senate. One of the local papers, acting on a tip, sues to unseal the divorce records.
 * 4) The unsealed records tell stories of Ryan bringing his wife to sex clubs against her will, demanding she have sex with him and strangers in public.
 * 5) Ryan withdraws from the race. His replacement loses the race to the Democratic challenger, a fresh-faced state senator named Barack Hussein Obama.
 * 6) Obama wins the seat, which had been held by Republicans for several terms.
 * 7) Four years later...

The Borg Queen is Seven of Nine's mother, cloned and altered to fit the Borg's needs, and Seven is needed as the perfect genetic match to replace her.
The relaunch novels specifically detail the "Royal Protocols", a set of instructions by the Borg to alter and adapt a Borg female into a new queen. As genetic resequencing is a possibility as part of the alterations (and, indeed, would make sense if the Queen is supposed to coordinate the individual thoughts of millions of Borg of mixed species), it wouldn't be surprising if those alterations transformed any species of Borg Female into Species 125, the Borg's own species of Queen. Also, Seven of Nine is expressly listed as a candidate in the Protocols, and the Borg Queen in Voyager certainly seems insistent on regaining her in any manner possible with her individuality intact, usually obsessing over her like a mother would obsess over their child. At one point, the Queen even deliberately taunts and tempts Seven with being reunited with her family using her assimilated father as bait (her mother is nowhere to be found, notably, and she isn't mentioned by the Borg Queen during the offer). Obviously, the Borg Queen being Seven's mother would make Seven the most suitable genetic candidate for succession, but the Queen's push to put her into that position means she still has some of her compassion and motherly instincts about her; she obviously has her individuality intact, as well, to perform her duties as the Queen, and she clearly wants her daughter to join in on the new family business.
 * This would also explain why Seven's ship (back before she was Seven) was taken by the Borg before the original timeline's First Contact, and why Seven doesn't want to consider herself human.
 * Does not compute. If I see a Zombie, I will kill it before it bites me. If they send a Zombie in my mother's body, I might hesitate, which gives it the chance to bite me; I might be so outraged by the blasphemy that I don't aim properly which gives it the chance to bite me: because I am an emotional Human. Borg purged Seven's emotions: she wouldn't weaken.

Tom Paris and Harry Kim are Voyager's One True Pairing
C'mon, it's practically Word of God anyway!
 * In the very least,

Fear's first victim died of a natural heart attack
In the Voyager episode "The Thaw", aliens inside a holodeck/cryogenic suspension machine are menaced by a creation created from their minds, a Joker Expy named "Fear". It's just a simulation that shouldn't be able to hurt them, but Fear has discovered he can terrify them into having heart attacks. Since all his power comes from Your Mind Makes It Real, he shouldn't be able to hurt them: They know the system is harmless.

But what if Fear discovered the heart attack "exploit" by accident? Perhaps one of the people inside the simulation had a weak heart and happened to die of natural causes while Fear was trying to scare him? Before this, Fear would have been just be a minor annoyance, a character created from their fears about the future with no real power. Once one of them dies, they'd be a lot more afraid of him, giving him more power (since he is a creation of their fears) and making his threats real: The people think he can give them heart attacks; therefore, he can.

Voyager's Deuterium Shortage Was A Cover-Up.
Basically, they ran out of a different material, but the fact that this material is used on Voyager Intrepid-class starships is top secret. Thus, the official transcripts changed its name to something more mundane (there is no guarantee that any type of censor beep used would be nonsense to every race in the Federation). This would imply that Voyager itself was a documentary In-Universe. There should have been a scene where this exchange happened: "Young Officer: Sir, looking over the Voyager records, I could never understand why they were always running out of Deuterium.

Older Officer: Well, that's because they didn't. The records were altered because what they did run out of is considered top secret. So, when they were talking about deuterium, they were actually talking about *obvious voice over* Deuterium.

Young Officer: Ohhhhh!"


 * Given the patent absurdity of running critically low on deuterium (an isotope of hydrogen, which makes up 75% of the universe), that makes perfect sense.

Species 8472 are an offshoot of the Vorlon race that colonised Fluidic space and eventually reached the TNG universe.
Just look at their ships!
 * The Shadows seem more likely.
 * Could be a group of Shadows and Vorlons that were stuck in Thirdspace after they closed the gate and eventually crossbred.
 * That would require Shadows and Vorlons to be able to stand each other.
 * Well, they do work together against the Third Space Aliens according to the movie. Maybe the group that got stuck there decided to keep at it, as they were trapped in hostile territory.
 * You get lonely, centuries pass. You can't get intimate with your blood relatives after all. And after a few beers your hated Neighbor down the road starts looking mighty fine...

"Year of Hell" paradoxed the entire universe out of existence; everything afterwards is a dream...
Or something...
 * It did create an extra copy of the Doctor -- um, Voyager's EMH...
 * What was always odd about the end of Part II is exactly how Janeway knew to listen to the Krenim and get out of there, versus being the Jerkass she was the first time around who ignored and taunted them.
 * She listened the second time because they said it nicely that time. The first time they ticked her off into wanting to defy them since they were so full of themselves.
 * It's another example of Janeway's questionable leadership skills in action. The decision on whether or not to risk the lives of her ship and crew by violating Krenim space isn't based on anything like consideration of the risk involved, but whether or not one person is a bit jerky to her. Even then, you'd think she might have tried negotiating with Nice Version for passage.

Seska from Voyager is the lost daughter of Legate Ghemor from Deep Space Nine
Her Obsidian Order deep-cover programming had an allowance for situations not listed in its parameters, thus enabling Ileana Ghemor/"Seska" to awaken once she was in the Delta Quadrant. Evidence:
 * 1) Even after she knew about Cardassian infiltration techniques and what to look for, Kira never found Ileana among Bajorans.
 * 2) Seska could not have been the spy's Cardassian name. It would have been recognized in a heartbeat by angry Bajorans.

The real Seska probably died during the Occupation.


 * Jossed as of the Deep Space Nine re-launch novels Warpath and Fearful Symmetry. Iliana was actually held captive by Dukat as a Kira look-alike sex slave for fifteen years.
 * Novels aren't canon.

Species 8472 are Protoss/Zerg-Hybrids, and the Fluid Space is what the Starcraft universe will turn into when Purity of Form and Purity of Essence are combined.

 * Does that make Kerrigan Rei?
 * Perhaps, but she could also be Asuka. Also, the Borg Queen is Motoko Kusanagi.
 * Wait....so Species 8472 literally zerg rushed the borg in delta quadrant?
 * Honestly, I thought they were more Protoss dominant.

Harry Kim and Naomi Wildman are actually the originals, and everyone else who was on Voyager during "Deadlock" are in fact the duplicates.
While being heavily implied that both of them are alternates, it was never outright stated or even mentioned again in the series. There is a fifty-percent chance that the Voyager they came from was the 'real' one. If so, they are the only two members of the original crew out of nearly a hundred and fifty to ever make it home.
 * Naomi was born inside the Delta quadrant, so make that only Harry Kim.
 * It's hard to tell if this is actually a Tear Jerker, or a Crowning Moment of Funny.
 * It can be both, as it is also very ironic that the resident Butt Monkey Harry Kim is the only original crew member that isn't a clone or otherwise didn't permanently stay dead.
 * What? Both voyagers were equally original, having split about an hour before one of them self-destructed. One thing it did do was create a funny report. A starship with 149 crewmembers has 150 casualties (Voyager A harry and Naomi A +148 voyager B crewmen) and 150 survivors.
 * Notice that the other Voyager started the proton bursts first, before 'our' Voyager had the chance to. Given that both crews and their experiences were exactly the same up to that point, this theory is actually very likely when you think about it. Regardless, one ship and crew was doomed from the start (both Janeways come to this conclusion later) and would have to be destroyed to ensure that the other survives, or else they would all die. At the end of the day though, there is a rather twisted Everybody Lives ending in a sense, and Harry Kim (while talking to Janeway) can't quite comprehend everything that has happened.

Kes went insane after leaving Voyager because she learned something she didn't want to know.
When Kes left in “The Gift”, her psychic powers had caused her to evolve into a higher life form (thanks to her experience with Species 8472). When she returned years later in “Fury”, we never learned what happened after she left that made her so bitter and so crazy. She blames Janeway for “filling her head with ideas of exploration.” Since Kes was always so eager to explore, she probably continued to do so after leaving Voyager. In her higher plane of existence, she must’ve learned something upsetting about life, the universe, and everything that drove her insane. Being reminded of who she used to be probably had the effect of reminding this now higher being that, "It's the simple joys of life that matter, not the big picture", or something cheesey like that.
 * Maybe Kes' power allowed her to perceive disruptions in time. Considering how Voyager messed up the timeline every few episodes that could have caused her a great deal of frustration or possible harm as the timestream kept altering back and forth.
 * Very plausible; as seen in "Time and Again", Kes really can sense changes in the timeline, at least sometimes. She could also sense the deaths of strangers lightyears away. Having both these abilities increased dramatically could easily have driven her over the edge.
 * Maybe her "transcendence" did not include her life span, and she got bitter that even though she was all-powerful, she was still so very mortal.

Kes went insane after leaving Voyager because she learned that the Borg had assimilated her world.
The Ocampa were a race that was completely defenseless and possessed massive psychic power, definitely something the Borg would want to add to themselves. They would have learned of the Ocampa through Voyager's many contacts with them (Tuvok was assimilated in full, Seven's memories were downloaded, they had a Collective in their cargo bay for several days which would have been ample time to learn of them). This would explain: -Kes' irrational rage. -her aiming that rage at her forme friends -wating to send herself home, likely out of a deluded desire to protect her people After she was calmed down she snapped out of shock, which she'd been in sense she becae aware of the destruction of her race, and decided to live out the remainder of her life, quitely.

Kes went insane because of the WMG from The Thing page
If you think about it this also makes somewhat a fair amount of sense in the bottom of the Thing WMG page there is a theory stating that most of the Real Life universe (outside of our galaxy) consists of nothing but Eldritch Abominations and non humanoid horrors like something out of a H.P. Lovecraft story Gone Horribly Wrong and only AscendedBeings and beings who become Abominations themselves could survive and there was nothing that Humanity or any other humanoid species (the Borg against species 8472 was more then enough proof of this) could do absolutely nothing to stop it.

Kes learned this little piece of Nightmare Fuel while ascended and slowly the truth began to drive her mad. After a while Kes returned (or was forced to return) to her corporeal (albeit aged) state and began to blame the crew of Voyager (especially Janeway) for ever even going to the stars to begin her evolution with the rest of her kind and learning this horrible reality. However interestingly enough this may lead to another theory...

The Q Continuum is the only thing keeping the Star Trek Universe alive
As is connected with the theory above according to Q himself (albeit he is a Unreliable Narrator) the Q probably already knew about the "Truth" of the universe yet still have a "meh" attitude about it (which unto itself is proof of how pretty powerful and truly Badass the continuum really is!). the Q probably eons ago came across the Milky Way galaxy and our little blue ball and slowly over time most of them (at least the ones who weren't complete JerkAsses) grew to have a soft spot for humanity and after a while decided to keep this area of space safe for a while.

This is somewhat proven by the TOS era as it appeared that some Eldritch Abominations were slowly beginning to creep in to our galaxy yet by the end of the Original series movie era they just..stopped with no real reason given as to why. the only explanation as to why is The Q basically they told the rest of the nearby universe not to mess with their region of space..or else. Boiled down it pretty makes us and the rest of the galaxy the Trek universe the Q Continuums Prison Bitch which oddly explains why Q himself wants humanity (Picard mostly) to grovel at his feet.

The Q Continuum is the only hope against mankind.
The Ultimate Question actually is “How many times did the Q Continuum have to restart the Universe after you maniacs blew it up?” This is the reason Q, during his first and last appearances aboard the Enterprise, put Humanity on trial and orchestrated our removal from History altogether. It was even a directive from the Continuum, where the Federation is later portrayed as a scarecrow and remaining human as the “second worst fate” a Q could possibly imagine. The eldritch abominations encountered by the old Enterprise have become rarer in the Alpha Quadrant because they learned about humans true horrifying potential. And of course, this is also what drove Kes insane after she ascended to a higher state of existence.

Neelix is a pedophile.
First, Neelix is dating Kes, who is less than two years old when the shows starts. After breaking up, he starts spending much of his time "taking care" of Naomi Wildman after she's born. He also spends quite a bit of time with the Borg children (along with Seven, whom he doesn't even seem to look twice at). Coincidence? Not on Wild Mass Guessing!
 * What persuaded him to leave Voyager? Meeting a Talaxian widow and her young son. Favourite target acquiring method of earth paedophiles? Date a mother who has no contact with the father of her children. Stardate 54868.6, Moral Officer's Log: Jackpot!
 * Kes is age 2 and lives 9 years, so at first, we assumed it was kosher. But then episode Eulogium stated that Kes did not expect to become sexually mature so soon.
 * Though for the Ocompa sexual maturity is different than physical maturity and doubles as menopause as well. We don't even have any evidence that Kes did or even could have sex with Neelix. Her reproductive organs are on her hands and she gives birth from a sack on her back, she probably doesn't even have a vagina.
 * Who says Neelix needs . . . I'm done speculating about their anatomy.

The Doctor's portable holographic emitter is the most powerful technology ever created.
Look, Holograms can do stupidly powerful things in Star Trek canon. Now we have portable ones that can be carried by holograms. All you'd need to do is make a portable emitter, and then have it project a much larger and more powerful holographic portable holographic projector. And behold a self-perpetuating series of mobile holograms. Even if you couldn't do that, you could easily have a holographic space ship crewed by holograms.
 * This was discussed in a Strange New Worlds story, where a mega-Enterprise is exploring outside the galaxy,
 * This wouldn't work under the given reasoning. A holographic portable holoemitter would still only be capable of emitting a hologram within the range of the original holoemitter, much as how a hologram that attempts to walk off the holodeck into the rest of the ship will disappear as it leaves the range of the holodeck's holoemitters. The holographic portable holoemitter would only be a projection, and thus any hologram created by the holographic portable holoemitter would actually be created by the original holoemitter, and subject to its limits. Remember, holograms aren't actually physical, they're pure simulation.

Seven of Nine was never part of the collective.
Note how different she acts from any other drone that we have seen, even before leaving the collective. When she is separated she is revealed to have great emotional dependence on the collective, even though this would be suppressed by the Borg. My theory is that she was a 'willing' drone, raised from a young age by the Borg and used for the rare non-aggressive interactions with humanoid species. Basically, the Borg brainwashed her and monitored her thoughts all her life.
 * This fits with the above theory that she was being kept around as a potential replacement Queen - they would need a free-thinking individual who honestly cares for the collective and would seek to protect and improve it at all costs, and were grooming Seven to fit that role.
 * Two things that don't work with this theory - first, if Seven was being kept unique intentionally, she wouldn't have been on some random borg cube sent to some random location, and then left for some time as one of only a few survivors when the cube was destroyed - note that, if it was a test or something, the borg would have appeared immediately after Seven demonstrated her capabilities, and the other survivors would have been reassimilated completely. Second, those other survivors show similar properties to Seven when we meet up with them, with the only difference being that they were basically permanently stuck connected to each other.
 * As such, it is possible that Seven was identified as a potential new Queen after the events following her cube's destruction, and began being groomed for the role, was provided further liberty to think independently at times, and was used as a representative of the Borg because of her initiative. However, she was a regular part of the collective prior to those events.

The Ocampa normally give birth to multiple children at once.
Most Ocampa pregnancies are at least twins, probably more (think litters). The reason Kes gives birth to only one child in the various potential futures we see is because she's giving birth to hybrids, which messed up the usual birthrate. Because otherwise, the Ocampan reproduction cycle just makes no sense.
 * This is given credence in one of the alternate history anthologies, where Kes and Neelix manage to have triplets.
 * Large litters wouldn't make sense for a race in which the females have just two breasts. But the Ocampa could easily be a case in which the females sequester the sperm from their single mating, and dole it out bit by bit over the course of their reproductive lives. Thousands of invertebrate species have that ability in Real Life, and the short Ocampan life span would make it easier to keep the stored sperm viable for long enough.

The crew deleted all Log entries concerning the Tuvix incident before Voyager returned home.
That's why Janeway was promoted to admiral after their return instead of being charged with murder.
 * And let's not get started on how she treated Seven (If you decide to return to the Borg, you lack the ability to decide whether you want to return to the Borg or not.).

During "The Killing Game," Naomi Wildman was...

 * ...in the WWII program, hiding in the attic of Neelix's house, singing "I Have A Little Dreidel..."
 * ...outside the holodeck with Harry Kim and the other slaves, serving the Hirogen lemonade and biscuits.
 * I'm going with this one, since the Hirogen were shown to be hunters with a rudimentary code of honor, and hunters usually do not consider immature offspring to be fair sport.
 * ...hiding in a Jeffries Tube, singing "I Have A Little Dreidel..."
 * ...in the Klingon simulation, sitting in a cave in full mock-Klingon makeup, singing "I Have A Little Bat'leth..."

Tom and Harry have a mutual friend Richard whom we never see because he stayed in the Alpha Quadrant.
... you saw what I did there.
 * That is evil. Congratulations! Vivat tertius petrus a sole.
 * Someone needs to write a Slash Fic called "Tom's dick and Harry".

Janeway is/was a member of Section 31
...and her real mission (after the failure of the Maquis pursuit) was to acquire technology, information and possible allies that could be used to defeat the Dominion and the Borg. That's why she destroyed the Array and stranded the crew in the Delta Quadrant in the first place, and why she either resisted or outright sabotaged any attempts to bring Voyager home and using any means necessary to keep the true nature of her mission secret (including murdering Tuvix who was slowly but surely figuring out her plans, reprogramming the Doctor whenever necessary and mind-frelling with Seven of Nine in The Voyager Conspiracy when she stumbled onto the truth). But when she was given the order to terminate Seven of Nine (after extracting all useful information from her), she refused because she had grown attatched to her emotionally to the point of obsession. Section 31 had the technology to bring Voyager back at any time, but when Janeway disobeyed orders, they cut off contact completely and left her well and truly stranded.

Shortly before Voyager returned in the original timeline, Section 31 planned to have her secretly executed but realized that she had taken measures to ensure that certain information would find its way into the "wrong" hands in the event of her untimely death, so they murdered Seven of Nine instead, using Pathfinder to send a code to disrupt her nanotechnology. In order to protect the rest of her crew, Janeway kept quiet, but ultimately decided to go back in time and "set things right" by not destroying the Array and allowing Voyager to return without incident. However, she realized that the information and technology she brought back was indeed crucial to the protection of the Federation, so she opted to go with "Plan B" instead and destroy the Borg in the process. Her promotion to Admiral in both timelines came about when she blackmailed certain top Starfleet brass (many of whom wanted to court-martial her after examining the mission logs and grilling her crew about certain questionable command decisions), and is now using her new position to destroy Section 31 from within.

Janeway = Sarah Palin
I always guessed that after conceiving of a female captain, the writers of Voyager leaned back and basked in their self-satisfaction, and never actually bothered with making her interesting in any way.

Sarah Palin, on the other hand...

Chakotay's "tribe" are just a bunch of new-age hippies.
Among the massive death and destruction of World War 3, the few remaining Native Americans were killed and the records of their actual beliefs and practices were mostly destroyed, leaving behind only a vague legend tarnished by pop culture. Centuries later, a group that included Chakotay's parents or grandparents gathered those legends together and decided to re-create "Indian" culture. They ended up with a bastardized, historically inaccurate version of it that they follow as though it's an actual ancient tradition.
 * So basically, it's Wicca all over again?
 * Daaaaaaamn! This troper is Wiccan and just spit coffee all over his keyboard laughing.
 * So the reason he's a Hollywood Indian is because he's from a group of Hollywood Indians? That explains so very much.

Tuvok's line in part 2 of the pilot about how it would take hours to get the array back online was inserted after initial production.
They thought after shooting "why didn't they just use a time bomb"? Realizing this plot hole, they reshot the scene where the Caretaker dies to include Tuvok's line. That's why in future episodes they kept acting like Janeway had this big moral decision "save the Ocampa and destroy the array" or "return home", when the choices were really "save the Ocampa and destroy the array" or "try to make a deal with hostile, untrustworthy aliens to give ourselves a slight chance of getting home". It wasn't part of the original series bible and no one remembered to write it down.

Tom Paris is the reincarnation of Captain Kirk.
There's a slight physical resemblance and they're both mavericks. Tom enjoys playing in Zeerust-laden holonovels where he gets to play the Big Damn Hero much as Kirk did, and when he had the opportunity he built a control panel with actual knobs and dials - a feature of Constitution-class ships. And how, you may ask, could Tom be the reincarnation of Kirk when Kirk died well after Tom was born? He violated temporal laws for the eighteenth time, that's how.

Dark Frontier was a stealth deconstruction of the idea of children on the spaceships
We see a loving family take their young daughter on a ship into space to contact a species they know incredibly little about and this results in their forced assimilation. It certainly sounds like someone writing it to subtly point out how stupid it is to bring young children with you to contact unknown forces when the universe seems to be filled with creatures trying to kill you.

Janeway allowed Harry Kim to come to the senior staff meetings out of guilt
It seems odd that Janeway would have allowed an ensign right out of the Academy to take part in critical meetings reserved for the senior staff. However, consider the fact that in the very first episode, Janeway was deeply troubled by the fact that she had separated him from his family in such a fashion. As an attempt to do some 'damage control' for her guilt, she 'adopted' Harry and tried to give him a new 'family' (the senior staff) in order to ease the pain of his separation. She singled out Harry for this treatment because he was the youngest and least experienced member of Voyager's crew after leaving the Alpha Quadrant.

The day after Voyager gets home, Seven of Nine is killed by slipping on a banana skin and Tuvok has a shuttlecraft land on him
It would just serve Janeway right for messing with the timeline.

Therapists or no therapists, Naomi still does not like things that buzz like insects.
She was just a baby when the macroviruses attacked. That would leave an indelible impression on anyone's psyche.

Most of the non-human crew members work Night Shifts.
In most episodes, most if not all of the crew members showing in the background appear human. But in episodes that focus on the "lower decks," the crew is shown as being very diverse, with Bolians, Bajorans, Vulcans, and Betazoids. We know these non-human crew members are on-board. So why don't we usually see them? Granted, Betazoids and Bajorans could both look like humans from afar (if you're not close enough to see their eyes or noses). So maybe those crewmembers have the same shift schedules as the humans. But what about the Bolians and Vulcans, and any other species that would be more noticeable?

They work night shifts. Why? Various reasons. Perhaps crew members from the same planet were more comfortable around each other, and preferred to all work the same schedule (some indirect, unintended segregation if you will). Or perhaps they have sleep schedules that work out best for the Night Shift (somehow).

Seska was mentally ill, and her only hope for a cure was in the Alpha Quadrant.
Up until "State of Flux," Seska, while shady, seemed a smart and mentally stable person. Come "State of Flux" however, and she begins to behave very irrationally. Yes, she is frustrated with Starfleet regulations limiting Voyager's return home; but surely a scientist and spy as brilliant as her would have realized that backwards space-cavemen like the Kazon would not be better help. Then there's "Manuvers," in which Seska either steals Chakotay's "DNA" to impregnate herself, or just lies and claims she did; either choice is quite odd, and never really explained on the show. After her death we learn (in "Worst Case Scenario") that, before leaving Voyager, Seska tampered with Tuvok's holonovel and made it deadly...why again?

Long story short, here's what we know about Seska: she is brilliant, with great problem-solving skills, as well as planning and scheming; she is DESPERATE to return to the Alpha Quadrant; and she makes bizarre, irrational decisions that are not in her own best interests.

Explanation: Seska was mentally ill. She was receiving regular treatment for her illness while spying on the Maquis, whenever she reported into her Cardassian authorities. But once lost in the Delta Quadrant, that treatment was gone. She struggled to keep a grip on herself and get home as fast as possible, but failed in both regards. (She certainly wouldn't be the first Cardassian Trekkies know to go crazy.)

Tom's duplicate in "Course, Oblivion" died by suicide.
We do not see Tom's duplicate die; last we see him, he is on the bridge, expressing his cynicism and wondering out loud why he's still taking orders from Janeway's duplicate. Come the next staff meeting, Tom is already gone. That last time we saw Tom, the decay had not affected him nearly as badly as some other crewmembers. There may have been internal damage that killed him soon after, but it's not a given.

Tom's duplicate had completely given up hope, once finding out he was a duplicate. Harry asks if Tom wants to try to reach Earth, or "just wait to disintegrate." Tom stares at Harry a moment, as if thinking about that.

After losing Chakotay, Tom decided that no, he didn't want to wait to disintegrate, and he had nothing to live for anyway. So he returned to his quarters and phasered himself.

Chakotay's recurring stiffness and monotone has an explanation.
Much of the time, Chakotay speaks and acts with as much emotion as anyone else. But every now and then, he becomes oddly stiff; he speaks in a monotone, sometimes even tired sounding, voice, and shows little to no emotion, in situations where one should show LOTS of emotion. Why? There are several possible reasons...
 * Long ago, Chakotay had a Spirit Quest that went horribly wrong. Now, every once in a while, he gets possessed by the ghost of Nicholas Cadge.
 * It's just one of his personal quirks. When he's under stress, he "freezes up," and becomes stiff and monotone. (Some people have this problem in real life.) For the most part he's gotten out of that habit, but it still shows up now and then.
 * Chakotay had a Spirit Quest gone horribly wrong, and is now aware of the Fourth Wall. For the most part he tries to ignore it, and do his duty as First Officer. But sometimes, he can't help but groan and what the writers beyond the Fourth Wall are doing--and the fact that no one except himself and Q suspects that they are actually fictional characters in a TV series.
 * Three words: Indian Peace Pipe.

Chakotay's is Seven's beard.
How do Chakotay and Seven go from having absolutely no chemistry together to a Last-Minute Hookup where they still have absolutely no chemistry together? Simple - they don't. The Seven/Janeway shippers were entirely right, but Starfleet disapproved of their captain's relationship with an underling still recovering from assimilation trauma, so Chakotay provided them cover.
 * So would that make Chakotay Treebeard?

The Krenim timeship has been holding the Borg at bay for centuries.
We know from the assimilated personalities living in Seven's implants that the Borg have assimilated Krenim in the past, it's entirely possible that the Borg have attempted to invade the area of space where the Krenim live on numerous occasions and always been RetGonned; each time they send a ship it gets erased until a scenario plays out in which they decide not to investiage/invade and that's the timeline that gets preserved