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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Star Trek: Enterprise
The Federation was a plot by Archer to acquire alien technology
Since childhood, Archer had harbored resentment towards the Vulcans for forcing his father to actually work to develop a fast warp drive, rather than simply handing him the technology on a platter. He continued to maintain this bitterness his entire life, and it only got worse as he encountered other alien species with more advanced technology than humanity had. However, seeing the Xindi cooperating (somewhat contentiously) to achieve their collective ends gave Archer an idea. If he could form a permanent "alliance" between Earth and other, more advanced, species he could make technology sharing an intrinsic part of that alliance by claiming it was all for the common good.

When he toppled the Vulcan High Command, his opportunity began to solidify. The less paranoid Vulcan civilian government underestimated Archer's cunning. Citing the recurring external threats that species in the region faced, he pushed forward the idea of the Federation and Starfleet as a common defensive strategy. Of course, such a strategy would work best if the Federation had the highest possible level of technology. So members were encouraged to be more open in allowing each other to study their tech. Since humans were one of the less advanced species, they benefited the most from this arrangement while giving up the least.

Archer played the mutual distrust of established space powers such as the Vulcans and Andorians like a musical instrument. Thus he was able to promote the idea of comparatively "primitive" Earth as a "neutral" center for this emerging Federation, and with a little politicking he managed to make it both the capital of the Federation and the headquarters of Starfleet. Humanity now had access to a wide range of alien science and scientists, who congregated in the new political/military center of the Federation. No longer would Vulcans maintain their technological superiority in secrecy.

The Federation has worked this way ever since. It uses its advanced technology as a lure to get new members to join, while cherry-picking new technologies from each new member species. The Prime Directive was Archer's tool for making sure that this arrangement perpetually worked to Earth's advantage. By prohibiting the sharing of technology without a world first joining the Federation, only those deemed to have something useful to contribute would receive anything from the Federation. The Federation was, of course, allowed to take and study any alien technology it could get its hands on.

That the Federation government, and most especially Starfleet, are dominated by humans is the key proof point. Archer was an obvious hypocrite for coveting alien technology and resenting those who refused to share it with humanity, even as he repeatedly withheld technology from other races (to the point of allowing extinction). Humans remain more passionate about the Prime Directive than almost any other Federation species except perhaps the Vulcans. This is because the system is designed to keep the flow of new technology pointed at Earth, while limiting the advancement of potential rival powers. Earth became the literal center of the Alpha and Beta Quadrants through clever theft of alien technology. They don't want anyone else doing likewise.

Humans started the Temporal Cold War.
We see four time in the star trek saga that humans were just like 'how would the honey badger handle the temporal prime directive?' 1- was when Kirk and the crew went back in time to get humpback whales, 2- was when Janeway and the crew discover that the computer revolution wasn't supposed to happen but did due to their temporal interference, now it wasn't their fault but they sure as hell didn't do a damned thing to correct it, 3- in the original timeline the Enterprise C never saves the Klingons and Kitomer, but they managed to alter and effect events because a purposefully temporal displaced Tasha Yar was there, 4- Janeway again in Endgame says fuck all to the temporal prime directive and goes back in time to destroy the borg collective. So in the future of the future somebody looks back on the records and is like, 'hey wait a minute, four times humans violated the temporal prime directive, each time drastically altering the time line so that humanity maintains their dominance in history.' So as the temporal accords state somebody should go back in time and correct these temporal incursions, but those future humans realize if they do they erase their own history of dominance, so they violate they accords and let the incursions stand and in fact go to 'war' against those who try to enforce the temporal accords against them.
  • The temporal anomaly in Yesterday's Enterprise was a random temporal anomaly...or was it. Really, of all the myriad vastness of the universe it's purely random chance that a ship named Enterprise is sent through time to randomly bump into a ship named Enterprise in such a way that just happens to randomly save the Federation from loosing war to the Klingons. I'm not buying it. the temporal anomaly in Yesterday's Enterprise was clearly a play in the temporal cold war.
    • Maybe the reason the Enterprise D encountered so many temporal anomalies was because they were near misses and/or sabotaged attempts at temporal incursions in the temporal cold war.

Enterprise is responsible for the Klingons having cloaking technology.
In the episode "Unexpected", when the crew relocates the Xyrillians, Archer and team convince the Klingons to not destroy the Xyrillians, but part of that deal includes giving the Klingons the Xyrillian's advanced Holodeck-like (yes, that Holodeck) technology. The Klingons proceed to ask "Can this technology be adapted to our power matrix?" Good work, Enterprise, you just gave the Klingons cloaking technology.

The Xindi were erased from history by the temporal cold war.
This is why there is no mention of such an important species in the history of humanity in any other Star Trek. We see Daniel's and Archer in the future watching the time line right itself, meaning the temporal incursions Archer encountered were now being erased and replaced with the timeline we know and love.

The events depicted in Star Trek: First Contact led to the creation of two divergent timelines from the Prime Timeline, in addition to altering the events in the Prime Timeline.
  • One of these timelines is the Mirror Universe

As extension of the above theory, the Temporal Cold War occurred as a direct or indirect result of the creation of the two divergent timelines.

Due to the Temporal Cold War, the altered historical events that are depicted in Star Trek: Enterprise occur in the second timeline created as a result of First Contact... which leads into the events in the film Star Trek (2009)
  • This timeline is essentially a Close Enough Timeline...at least until Nero arrives from the Prime Timeline...

In Star Trek: First Contact, the Temporal Cold War or the Spherebuilders mucking about with time have changed history enough to put Enterprise in an alternate timeline from the "main" Star Trek timeline.
Consider the last Enterprise episode, which is an attempt to show that Enterprise is in the main timeline. Riker, after talking with Enterprise crew on the holodeck, decides to reveal the cloaking device conspiracy (from the TNG episode "The Pegasus"). But in that TNG episode, he doesn't reveal the device before he visits the Pegasus. He doesn't reveal the conspiracy until he is forced to by the Romulans. Unlike in the original timeline, the history of the NX-01 crew convinces Riker to go ahead and reveal the plot instead of wavering until his hand is forced.
  • Further evidence: A number of crew members in Ten Forward at the start of These Are The Voyages... have the flat collars used in the first few seasons of TNG - but The Pegasus occurred in Season 7. By then, everyone in the main continuity had the stand-up collars.
  • Additional evidence: The ship is named Enterprise. Later-era shows give Enterprise counts that include only NCC 1701 through 1701-E. Zephram Cochrane, Lily Sloane, and others were told during Star Trek: First Contact that Picard and co. came from the Enterprise; this influenced the later naming. It may also have influenced the design; Lily spent a lot of time in the Enterprise-E. design, including places usually reserved for engineers.
  • The Voyager episodes "Hope" and "Fear" suggest that the pre-First Contact timeline's NX-01 was named USS Dauntless. This dovetails nicely with the mirror universe ISS Avenger.
    • Also see the "NX-01 becomes the NCC-1701" suggestion below.
  • It is only this episode that is in an alternate timeline (and that stupid gothic-romance-IN-SPACE episode from Season 3), not the whole of Enterprise.
  • Given that a picture of the Enterprise NX-01 appears on a wall in Star Trek: Nemesis, it can be taken that Enterprise is in the past of the "prime" Star Trek timeline. So maybe "before" the events of Star Trek: First Contact some things had been different (e.g the name of the ship, the design of the ship, whatever), but "after" First Contact the timeline had been changed to fit what's shown on Enterprise — and this is the "real" timeline, not an "alternate" one.
    • Perhaps Nemesis happened in a Close Enough Timeline. The TNG films after First Contact have been accused of giving their leads Character Derailment. If those happened in a different timeline than the main TNG series, then that is explained. And this makes a nice divergence point.
      • The point is that there have been a million and one examples of Close Enough Timelines in Star Trek — First Contact being just one of them. In each case, the Close Enough Timeline becomes the official Star Trek timeline from then on. So Enterprise having had the events of First Contact take place in its past does not mean it's set in a different timeline (which somehow delegitimises it in the eyes of the Fan Dumb) — it means it's set in the latest version of the correct timeline.

The mirror universe is the 'normal' timeline.
The opening of In a Mirror Darkly shows Earth's first contact with the Vulcans. Picard and co are nowhere to be seen. That's because in this universe, the events of First Contact never happened, so the Enterprise-D crew never travel to 2063 and reveal to Cochrane the potential of his invention, which would have resulted in the push to explore and the creation of the Federation. When the Vulcans land, Cochrane just assumes they're evil alien invaders and kills them. Earth then pushes to aggressively expand its territory in order to defend against future invasions. The regular Trek universe was essentially brought about by the actions of its own inhabitants.

Enterprise is a Show Within a Show.
In the 24th century, a video/holodeck franchise is created based loosely on the adventures of Archer and company. It doesn't try too hard for accuracy and has three strikes against getting things right to begin with:
  1. It is based only on what has been declassified, the rest being pure guesswork.
  2. Internal-sensor recordings were nowhere near as complete then as later.
  3. over two hundred years, the NX-01's exploits have become legend.

This could easily explain the presence of TNG-and-later aesthetics, spotty production values, shouting Vulcans, and continuity issues. The real story of the Enterprise NX-01 has not been told.

  • This would also explain how this one ship somehow manages to blunder into every signature species or technology of the 24th century, none of which rated even a passing mention in the Kirk era and at least one of which was unknown at the beginning of Picard's era. It explains how that same ship was directly responsible for much of the political landscape of the quadrant. And it explains why that ship just happened to be named "Enterprise," as if the name itself always meant something special. It's just like when modern-day stories of the medieval period feature gender equality and good hygiene, or when medieval authors described Greek warriors as fully-armored knights with lances. Enterprise is nothing more than a historical retcon that takes 24th-century stuff for granted.
  • There seems to be a theme here...
  • Another possibility? Someone, say Q, altered all the records of what really happened simply for shits and giggles.

"These Are The Voyages..." is itself a Show Within a Show that Riker and Troi made under duress.

The novel The Good That Men Do basically took this concept and rolled with it, but even if one discounts the book, every charge of inaccuracy it levels against the holodeck simulation is credible, and supports the claim that it's a fake record. However, one may note that Riker and Troi are also a bit older and heavier than they were in the TNG episode "The Pegasus" and that Riker didn't actually go through with his supposed decision to tell Picard everything he knew about the Pegasus until the situation forced him to talk.

I think the last episode is also actually an inaccurate holodeck history, and that Riker and Troi deliberately inserted clues to its inaccuracy because they were being forced to make it, and wanted everyone who saw it to know the history they were portraying was just as false as the history it showed them supposedly viewing. Hence, they allowed the program to show them using advances in the holodeck technology that hadn't occurred yet, didn't adjust their appearances to look any younger than the age they actually were when they made this story (many years after the actual Pegasus incident), and subtly undermined the whole purpose of this fake history in every way they could.

Enterprise is in a parallel universe
This universe diverged from the universe we know after the events of First Contact.
  • Except that time travel in Star Trek does not work that way. Any changes that were made as a result of First Contact have become part of the "prime" timeline, Cosmic Retcon style. The episode "Regeneration" does indicate that the events of First Contact (with Picard's crew and the Borg) did happen in this series' backstory, but that doesn't make it a "parallel universe to the one we know" — it is the Star Trek universe we know. Deal with it.

The time travel aspect causes the two universes to be linked, leading to...

Enterprise is the history of the Mirror Universe.
This is pretty much Jossed, but think about it anyway. This theory is partly cribbed from William Shatner's Mirror Universe Trilogy, wherein Cochrane, who now knows about the Borg, realizes that there is danger out there and decides to explore much more carefully. It comes down to a coin toss.

Now, look at Enterprise. Within four years from beginning to explore deep space, how many Big Bads have our guys run into? It's easy to see them being pushed too far and becoming overly defensive, turning the Federation into the Empire.

So why is there a Mirror Universe episode in Enterprise? And why is Riker playing Chef on the holodeck? Because we're seeing a holonovel of MU history smuggled out of the mirror universe, and the MU episode is a red herring.
  • It is canon that the Star Trek universe has more than one parallel. (See the TNG episode "Parallels.") The 'mirror universe' episode of Enterprise just tapped into yet another one. And it seems oddly fitting that a terrible show should be consigned to the Mirror Universe. That there's more than one parallel Mirror Universe? Okay.... oww.....

The Mirror Universe version of Those Wacky Nazis were good guys.
  • The alternate opening for "In a Mirror, Darkly" shows a Luftwaffe plane getting shot down. Maybe in this reality, the Axis had no racial supremacy agenda. They still used the swastika, but in it's classically benevolent context. They still lost, though.

Enterprise's Evil Future Guy is Jonathan Archer.
The key is part two of "Shockwave". For most of the episode, Archer is missing. During this time, Silik is unable to contact the Future Guy, something he has no trouble doing when Archer is in his proper place in the timeline. Archer comes back through the Future Guy's machine — a strong hint for viewers.

Enterprise's Evil Future Guy is Crewman Daniels.
  • He's playing both sides to ensure that history happens the way he thinks it should.

  • It makes sense. The Temporal Cold War is The Last Great Time War we hear so much about, "Ninth Doctor" on. The "Temperal Operatives" are the Time Lords!
  • At one point, Archer asks Daniels if he's human. Daniels smiles nervously and says, "More or less...." At the very least, he's part Gallifryan!
    • Daniels's nervous demeanor in general is actually quite reminiscent of many of The Doctor's more quirky incarnations....
    • So is Archer his reluctant "companion"?

Noonien, and a few intervening generations of Soongs, are clones.
Arik was a geneticist, after all.
  • Bringing Khan Noonien Singh into this is just going to confuse things even more, isn't it?
    • Not really; Khan was cryo-frozen and launched into deep space in the 1990s, while the Soong family spent several generations devoted to research, first in genetics, and later in cybernetics. The only connection between the two is the similarity in the names, which was caused by Khan and Noonien being named after a friend of Gene Roddenberry.

The Spherebuilders powered the Xindi's subspace vortex system.
The Xindi could quickly teleport entire ships half way across the galaxy, a feat that only Sufficiently Advanced Aliens can do in later series. The Xindi are friendly with humans at the end of the Xindi arc, but they never show up again; you'd expect that a race that could travel that quickly would be somewhat important in the future of the galaxy. Nor does the Federation acquire their technology.

A simple explanation for this could be that the Spherebuilders (who were known to give technology to the Xindi) gave them a device that transported their ships in and out of Spherebuilder-space, allowing them quick travel across the universe. Once the Enterprise destroyed the spheres, the Spherebuilder realm collapsed and the device no longer functioned. The Xindi were stranded in their corner of the universe with ships that could no longer travel at high speed.
  • But the Aquatics returned Enterprise to Earth after the sphere network was destroyed.

A Xindi Civil War still takes place some time after the Xindi arc in Enterprise, and at least one of the five Xindi species we see in Enterprise will be extinct by the 26th century.
When Daniels takes Archer 400 years into the future to show him the battle of Procyon V, he reveals that there are Xindi serving aboard the Enterprise-J...but notably does not say which Xindi species. At the end of the Xindi arc on Enterprise, it looks like the Xindi council will be re-formed, with there being a line about how the Reptilians will have to re-join, given that even the Insectoids have now aligned with the others. However, we've seen that at least some of the Reptilians think they alone are the rightful leaders of the Xindi; they may not be willing to join their brethren, even given a four-against-one scenario. Or, since the Reptilians had turned on the Insectoids when the latter began to question the former, the Insectoids may not be so ready to forgive and accept the Reptilians as the other Xindi species are. Either way, the Xindi civil war is still coming, and which Xindi species are still alive in the 26th century, let alone serving on the Enterprise-J, remains uncertain.

The Xindi, or one sub-race of them, are the same race as the Kzinti
The Kzinti, from Star Trek: The Animated Series (as borrowed by Larry Niven from his own universe), are the Felinoid variant of the Xindi race, cast out years before for some reason. When Chekov refers to there having been a war with the Kzinti, he's referring to the war with the Xindi as displayed in ST:ENT. Presumably, the Kzinti Felinoid branch of the Xindi were discovered by humans afterwards, the whole thing was put together, and Chekov didn't bother with knowing that they weren't all together or that the felinoids had nothing to do with the Xindi war.

It makes sense. LOOK AT THE NAMES! Even better, say them — they are near-homophones!

The I.S.S. Avenger was named for Grand Admiral Solo's flagship from The Revenge of the Jedi through Legacy of the Force.
We know that they had similar stories in the Mirror Universe, but darker and with considerable Values Dissonance.

Dr. Sam Beckett quantum-leaped into Captain Archer and got stuck there
Okay, so Sam can only leap within his own life time. However, with an IQ of ~200, who's to say that he didn't find some way to extend his lifespan to ridiculous proportions? Also, with his wide array of expertise, Sam could have been destined to solve a great number of problems before the next leap—problems that extended beyond the timeline of the show.
  • Given that the original show had him leap into one of his ancestors, it's possible that he also leaped into a descendant. Of course, that means that Al is also in every episode, probably confused as hell at the technology around them and wandering off to spy on T'Pol whenever Archer needs him most.

Dr Noonien Soong from TNG is indirectly named after Khan.
It's canon that Dr Noonien Soong is the great-grandson of Dr Arik Soong, the villain from the three-part Augments story. I figure that Dr Arik Soong had a son whom he named Noonien after the most notorious of Augments, Khan Noonien Singh. The Dr Noonien Soong we know from TNG would thus be the namesake of his grandfather, who was himself named after Khan.

NX-01 becomes the NCC-1701.
The NX-01 was a testbed ship for new technology. It was the first Warp 5 starship, it got refitted with better weaponry to combat the dangers of deep space, and then Drex Files shows us schematics of it being fitted with a secondary hull in the never produced 5th Season. It's not far fetched to extrapolate that whenever improved technology is developed, it was tried on the testbed ship, and thus little by little it became the prototype for the Constitution class.

Why the extensive refit in ST:TMP instead of building a completely new ship? Testbed for the new hull type. Other Constitution II ships were later built according to the data gathered from its performance.

The M-5 computer? Testbed. The husky female computer voice? Testbed.

This is why the ship was being retired in ST3:TSFS, although the Admiral got the years wrong: the Enterprise was not 20 years old, but 120.

This also explains why the new Enterprise felt so strange to Scotty in ST5:TFF. It was built directly into the Constitution II class, so it lacked all the legacy structures that the old one gathered during its long history.

And finally, this explains why the NX-01 was never mentioned in the other series, despite its importance in creating the Federation: it was always there, right from the beginning!

The Valakians and Menk from Dear Doctor will eventually become...
The Breen and the Pakleds, respectively. Stolen from SF Debris's review, because it is mind-blowing.

First Contact and subsequently Regeneration changed the borg collective
  • We start with the original Borg, who understand and adapt technology and are a single species.
  • original Borg assimilate a computer on the enterprise E
  • Original Borg see how special humans are, with the frequency in which they find rare cosmic phenomenon, encounter super-powerful creatures and encounter odd instabilities in the timeline and yet constantly come out on top. We'll refer to this phenomenon as humans being lucky.
  • Deciding that Humans Are Special , they determine them to be the only species worthy to also be Borg
  • The original Borg create the queen and her private collective with the specific task of understanding humans and assimilating them. The queen has more imagination and listens to her impulses and emotions more to emulate humans. Her private collective consisted of a single cube.
  • The queen has her private cube assimilate Picard
  • The queen's cube is destroyed in the battle at Wolf 359 and Picard rescued
  • The Original Borg recreate the queen with her knowledge and memory intact. They give her a new private collective and she equips the drones with nano-probes capable of assimilating humanoid species.
  • The queen's new cube attack Earth, assimilating several (federation only) species on the way
  • The queen plans fail when her cube is destroyed and she decides to attack Earth in the past
  • During the events of First Contact the queen gets killed and all her drones get destroyed, with the exception of a few in the Antarctic, who merely got lobotomised
  • The lobotomised drones forget that their private collective wasn't the entire collective and lose much of their intelligence.
  • The events of regeneration happen and the Borg send a signal containing information about their present state to the original Borg. They use an encryption to make it appear on the surface as just being a set of stellar coordination
  • The original Borg, thinking that the message contained the secret to human luck, adapted everything the message said, turning them into the new Borg, as shown in Voyager.
    • So now there's an in-universe reason why the Borg started sucking in Voyager due to First Contact? That's actually...pretty neat.

Mirror Archer suffers from Clarke's Syndrome...

This actually has solid evidence to suggest this may be a possibility. Clarke's Syndrome, the disease that claimed the life of Henry Archer, could have certain genetic factors that could lead to Jonathan being predisposed to contracting it. The symptoms include pain and hallucinations, the latter of which Mirror Archer is seen to have of regular Archer. That he doesn't even seem to be surprised he's seeing him could be because such things are normal for him. That he seems to be gnashing and grinding his teeth all the time could be a pain symptom. Having a stoic Spartan resolve to suppress this pain would definitely be in keeping with the Mirror Universe.
  • This also might explain his resilience in the agony booth prototype. Doctor Phlox was quite openly impressed: "Ten hours in the booth!" If Mirror Archer was constantly in pain from Clarke's Syndrome, that booth might have been only mildly worse than what he had regularly been suffering all along.

Denobulans were related to the Cardassians...
Their facial ridges are similar enough to indicate at least some shared ancestry. We never saw them "before" Enterprise because they had been exterminated by their Cardassian "cousins" through ethnic cleansing campaigns. This also explains why the Federation would not only fight a war against the Cardassians, but why years later many people in the Federation still vehemently hate the Cardassians. Genocide against a founding member of the Federation would have that effect.

Information about the voyages of the NX-01 are spotty at best, due to:
1) War with the Romulans. Many colonies were destroyed and records were lost. Possibly the records on Memory Alpha (or its predecessor.)

2) Shoddy record-keeping by the Federation itself.

3) Supression of information by Section 31.

4) Revisionist history due to millions of people writing Fan Fic holographic programs over the intervening 200-plus years - which explains Trip getting pregnant.

Dr. Arik Soong is Dr. Noonian Soong.
They look identical, and Arik Soong is familiar with the Briar Patch, which has a convenient Fountain of Youth Planet in it. It's possible that after his release from prison, he traveled back to the Briar Patch, stumbled upon the Ba'ku world, and developed his positronic brain technology there, before leaving almost two hundred years later and resettled with a new identity on Omicron Theta. He hyped the technology a lot, but the prototypes failed for some reason, so was ridiculed out of the scientific world. Also, The Ba'ku know an awful lot about positronic brains, despite being technologically isolated for centuries.

President Archer is remembered as the worst leader in Federation history.
In the Mirror Universe episodes, it is mentioned that the real Archer was the President of the Federation for eight years (assuming they have a four-year system, that's two terms). Considering his behavior in "A Night in Sickbay", where he brought his dog to a delicate negotiation for a vital piece of equipment, I think Archer ended up having the worst presidency in the history of the Federation, something that exceeds James Buchanan, Herbert Hoover, and Jimmy Carter in dreadful leadership.
  • Extension WMG: they must have eight-year terms. The alternative is that Archer somehow got re-elected.
    • Other possibility was that archer ran against that dog. The election was one by one vote, and that was because the dog hit the Archer button by mistake.

A spy within the Starfleet WANTED the Enterprise to be a disaster

Somebody high within Starfleet wanted humanity to fail to get to the stars, to trigger as many wars with other races as possible and get destroyed. So, he or she (a Romulan spy or a somebody else posing as a human) used their influence to get the dumbest bunch of incompetent morons who applied for Starfleet to run the ship, and made the dumbest of them all the captain. Sadly sheer dumb luck allowed the Enterprise to be somewhat of a success.

M. Fincke and T. Virts are the identical descendants of the astronauts who played them in the episode.
They were inspired to join Starfleet by the stories they heard about their 21st-century ancestors' missions in space. I don't know, it's sort of nice to imagine.

The reason why Archer's ship wasn't in the pictures of Enterprise in TMP was because at that time, he was written out of the history books for his complicity in the Valakian genocide.
It was discovered that he intentionally withheld a cure that would have helped save a sentient species, and so, disgusted by this, while not written out of the history books, had his monuments torn down (the Prime Directive having yet to chrystalise into its dogmatic state). However, he was reinstated later when it was realized that Phlox's so-called cure would have been about as effective as a sugar pill because of the numerous mistakes he makes with regard to all sorts of sciences in that episode. Archer is written down as having made a bad decision but was being given terrible advice.

Everything in the series is 100% accurate, every other series simply had it's facts wrong
Because after realising that time travel was real and messing with the timeline a serious threat they decided to start falsifying their records about interactions with aliens in order to make the timeline harder to disrupt. Only a certain, top clearance, group of Starfleet officers have access to the real records and they eventually become the future time police. This practice either stopped once Starfleet became confident their timeline was sufficiently secure or it continues to thsi day, explaining every continuity issue in the entire franchise. Naturally, the finale was based off the false records, as it was nothing more than a holodeck simulation, and is thus complete nonsense.

Everything is just a nightmare Captain Kirk had while he was asleep onboard the Enterprise.
Because after he had one too many weird experiences, he decided to set up a [1] version of himself in charge and a bunch of other weirdos.

Shows like Revolution are actually holodeck simulations.
When you're a member of the Enterprise or Starfleet, encountering weird things is in the job description. The holodeck is an excellent way of preparing for all types of scenarios, no matter how unlikely they are to occur. In fact, Starfleet members would be in for quite a challenge if they ended up in a world that had all its electricity absorbed by nanites and everyone is fighting for dominance.
In the Twilight episode, Captain Archer has a bad case of Hinamizawa Syndrome, a Series:Higurashi no Naku koro nidisease caused by parasites.
He is infected with parasites that have no cure, he doesn't remember things people say, and he becomes increasingly violent and paranoid. Not only that, he seems to misinterpret things people say in this episode and seems to be quite, frankly losing his mind. Higurashi characters with this disease experience both mental and physical symptoms, including paranoia, talking to oneself, thinking someone is after you/lying to you, strange changes in mood and personality, sudden inclinations to violence, thinking parasites are inside your body. The thing is in Higu, Rena actually believes there are parasites in here-and she's right, too. The Hinamizawa parasites must have gotten onto Captain Archer somehow-and are affecting his mind.
The repair station in "Dead Stop" was built by the Breen.
We never did learn who built that station or why, but we do have some circumstantial evidence:
  • When Archer and his crew first scanned the station, they found it to be filled with a liquid helium atmosphere; helium has to be at temperatures very close to absolute zero to exist as a liquid, and T'Pol did mention how low the temperature was. Who's known (in later series) for being from a frozen planet and therefore being experts on cryogenics and refrigeration? The Breen, that's who.
  • The Breen are known to be reclusive, secretive, and treacherous in their dealings. (Weyoun, for his part, wondered why they needed refrigeration suits, since what he saw of their planet seemed quite temperate to him.) The station is also remarkably secretive and treacherous, "playing dumb" in response to the various characters' more probing questions even as it reproduces Archer's voice perfectly to trick Mayweather into walking into a trap. The station obviously has the same personality as the Breen, and that's because they're the ones who programmed it. Its motives are just as inscrutable as their own.
  • While several victims found on the station are from species to whom humanity hadn't even been introduced yet (including a Cardassian, for one), none of them are Breen. Why not? They built it, that's why; of course they would know about the station's "hidden fee" and would leave a back door to allow themselves to use it free of charge. They probably use it to take samples so they can study the psychology and physiology of other species and tailor their diplomacy and weapons accordingly. Only a few species with an innate distrust for bargains that seem too good to be true (the Ferengi, for one) probably ever managed to avoid losing a crew member to the station, and even so it probably still has some exquisitely detailed information on them from its sophisticated scanners.
The Temporal Cold War is now the go-to explanation for any continuity gaffs.
Any continuity gaffs in Star Trek? Nope there are no continuity gaffs in Star Trek, they are all actually fall out from temporal incursions left over from the Temporal Cold War. In fact this fallout applies to even shows outside of Trek...either that or shows outside of Trek are actually within Trek continuity. For example, on Cheers Frasier says both of his parents were psychiatrists and he is an only child...then when he gets his own spin off series we meet his cop father and his brother...well obviously this was fall out from a temporal incursion. On the 80s tv show Different Strokes they had an apartment and that apartment had a door in the back, and every frickin season that door led somewhere totally different than the season before, continuity gaff, NOPE, fall out from a temporal incursion from the Temporal Cold War. See it works for everything.
Every incident of time travel leaves a temporal anomaly in it's wake.
First Contact gives us an important insight to the after effects of time travel. So we see in First Contact that the Borg create a time travel portal and jump through it, and that leaves a hole in time, i.e. a temporal anomaly. However warp engines, by their nature, cause temporal anomalies to collapse but only if you go through them and back, closing the hole at both ends. In First Contact the temporal anomaly was closed relatively soon after it's formation so it didn't drift far. However let's say someone time travels and the resultant anomaly that spins off isn't closed quickly the anomaly wanders off randomly into space, but being an energy phenomenon it can travel faster than light and end up anywhere. So all the temporal anomalies the Enterprise(s) encounter are left over from some other ship or event time traveling. Also Anarax's temporal weapon probably shot off temporal anomalies all across the galaxy every time he fired it.

Humans WEREN'T ready for interstellar missions.
This isn't a WMG as much as a justification or response to some of the criticisms of the show. We see some pretty Benny Hill action from Starfleet, Archer and his crew. In Broken Bow Reed complains they beamed up the wrong supplies, REALLY, one starfleet's most important mission they couldn't get the supplies right. When the Enterprise meets their first alien species Archer just kind of rambles on, so apparently Starfleet had NOOOO protocols or procedures on how to make first contact, the whole point of the mission...REALLY!? In Strange New World they visit their first alien planet, and all they do is dick around, walking here and there and camping out. On and on. However remember in Broken Bow, Archer pushed for the ship to launch and take Klang back to Kronos. The ship WAS NOT ready to go, even Admiral Forest said so. Archer just pushed for the mission, and Starfleet agreed to send the Enterprise to take Klang to Kronos, and they launch it immediately. So, they really weren't ready for their mission. It was a spur of the moment decision, which the Vulcans thought was assanine. Then once the ship dropped of Klang, it just took off into deep space on it's mission. The ship WAS NOT ready. While we later learn that the Vulcans had a fear of humans and that is why they were holding them back, the facts is, Enterprise WAS NOT ready for it's mission, but Archer's obstinance won out and the ship went off into deep space before Star Fleet had properly equipped the ship, and before Star Fleet had put into place the proper protocols and procedures for a deep space exploration mission.

The 23rd century portions in "These Are the Voyages..." are also a holodeck program.
This explains why Riker and Troi look visibly older. The program is a bit inaccurate.

This show is a sequel to Quantum Leap.
After Quantum Leap, Sam Beckett discovered a way to leap to the future. He ended up in the 22nd century, where he inhabited the body of Captain Jonathan Archer. The real Archer does not resemble Scott Bakula, that is just how the audience sees him when Sam is in his body. The Future Guy is Romulan as Braga explained, but Sam inhabits his body later on as well, which is what Braga meant when he said that Future Guy is Archer.
  • In that case humans probably started the Temporal Cold War with advanced versions of the Quantum Leap technology which would insidiously let time travelers infiltrate any level of your society.

The Vulcan versus Andorian conflict began because of Delta Vega
In the 2009 Star Trek, Delta Vega is an arctic planet in the Vulcan System. It is understandable why a species like the Vulcans, who evolved on a hot, dry, planet, would not colonize such a world even though it was technically inhabitable. The environment was, however, absolutely perfect for Andorians. Since the Vulcans did not seem to be using the planet for anything, the Andorians may have wanted it for their own colony. Especially if they learned about it back when their ships were slower and could not travel as far as they could in later years. But since it was so close to Vulcan, and the Vulcans are not overly-sociable, they would not want another species colonizing within their star system. This escalated into a dispute between the Andorians, who felt that the Vulcans were wasting a perfectly good planet, and the Vulcans who did not want the Andorian "Empire" claiming territory near their homeworld. Eventually it progressed into full-blown hostility.

The Menk will become evil because of Archer and Phlox's decision
The Social Darwinist stance taken by Archer and Phlox in "Dear Doctor". Justified by the pseudo-scientific hypothesis that Goal-Oriented Evolution is driving the Valakians to extinction because Evolutionary Levels are supposedly a real thing and the Menk have the potential to become "more evolved" than them. A common defense of Prime Directive philosophy is that you don't want to "create a new Hitler" through well-meaning interference in a species' development. But, the Menk are already sufficiently sentient that the Valakians employ them in various jobs, in addition to caring for them generally. What will be the cultural impact on the Menk of watching their sibling species, a whole advanced civilization that has treated them nicely, die within a short span of time such that they will be up to their armpits in the corpses of the dead! What will this do to the psyche of their people as they evolve into "more advanced" beings? Odds are, in order to survive the massive psychological trauma, they will become callous. Also, xenophobic, since aliens came and offered no help in curing the dying Valakians. Will some of them make the logical connection that attacking the aliens and taking their technology by force rather than peaceful request might have saved the Valakians? If so, then their probable belief will be that when you need something you don't ask nicely, you take it forcefully. Otherwise you may not get what you need. Since they will have to be left wondering if what happened to the Valakians could happen to them too, they will likely evolve such a paranoid, violent, society.
Star Trek: Deep Space NineWMG/Live-Action TVStar Trek: The Next Generation

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