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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.
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:
Enterprise is in a parallel universe
This universe diverged from the universe we know after the events of First Contact.
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.
The Mirror Universe version of Those Wacky Nazis were good guys.
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.
Enterprise's Evil Future Guy is The Master, and Crewman Daniels is the Doctor's next incarnation.
Noonien, and a few intervening generations of Soongs, are clones.
Arik was a geneticist, after all.
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.
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.
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 Sci Fi 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.
- original Borg assimilate a computer on the enterprise E
- Original Borg see how lucky humans are
- 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 discovers that the entire damn federation is lucky, but the humans still are at the top
- The queen's cube is destroyed 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 encoded it as merely containing the location of Earth as security)
- 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.
Mirror Archer suffers from Clarke's Syndrome...
- This actually has a few things 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, which Mirror Archer has, with his vivid hallucinations 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 gnaw his teeth all the time could be the pain symptom. Having a stoic Spartan resolve to suppress it, would definitely be in keeping with the Mirror Universe.
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.
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