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Not all of Picard's Borg implants were removed.
He can hear the Borg because he still has receiver hardware installed in his brain that allows him not just to pick up the Collective's communication stream, but decipher and understand it well enough to glean the specific information he needs from it. Presumably, while Dr. Crusher and Starfleet Medical did the best they could, some of the Borg hardware was too deeply integrated to be safely removed.

  • Isn't there a line in the movie or in an episode where Picard says "I have their devices within my body?"

Picard not wanting to destroy the Enterprise is more than just revenge.
He was keeping a promise he made to Kirk, not to let anything getting him off the ship.

The Crew of the Enterprise is the source of divergence into the Mirror Universe.
The Enterprise crew was present to ensure that the events of First Contact went off without a hitch. Along the way, they managed to inspire Zefram Cochrane with tales of the future and how humanity manages to get past the post-apocalyptic hell-hole they are currently in. Thus informed, he greets the Vulcans in peace. Now, imagine how Zefram would have been with no Borg attack and no Enterprise crew there: a drunk depressed asshole living in the remains of what was once a superpower nation's nuclear arsenal. When aliens descend from the sky, using a highly advanced starship with who-knows what kinds of weapons to use on the poor, insignificant humans, odds are that he would react in a more wary, more paranoid, perhaps more violent manner (perhaps by shooting said aliens with a sawed-off shotgun and looting their ship) due to fears over what will happen now that highly advanced aliens have landed in the aftermath of World War 3. Thus, the crew Set Right What Once Went Wrong and ensured that the main timeline, rather than the mirror universe, became the 'prime' reality.
  • This is presented exactly that way in the beginning of Enterprise's "In a Mirror, Darkly" two-part episode: the Vulcan ship lands, the Vulcan greets Cochrane, and then a refilmed version of the scene shows Cochrane (or his hand double) drawing a gun and shooting the Vulcan before the rest of the crowd rushes forward to loot the ship.
    • Actually, this theory is Jossed by "In A Mirror Darkly". Mirror-Phlox clearly states that he's looked at the historical records of the USS Defiant NCC-1764 and found that there never was any specific point of divergence between the two universes throughout recorded history. The timelines moved in parallel but were never the same, with the Mirror Universe's history always being distinctly more brutal than the "main" universe (with the exception of the works of William Shakespeare). The opening sequence with Mirror-Cochrane simply illustrates the difference between the two universes.
      • We only have Phlox's reading of the Defiant's records to suppose that, though. The Mirror Universe inhabitants' understanding of history could well be coloured by the Imperially-sanctioned narrative of history which, in such a tyrannical society, is bound to be pretty heavily revisionist, possibly even to Nineteen Eighty-Four levels of wholesale rewriting. This might likely extend to classic literature.
      • Then again, that theory is also Jossed by Discovery, in which Mirror Universe Terrans are somehow more sensitive to light than those in the Prime Universe. That could (probably) only have happened at an earlier stage of human evolution predating recorded history.
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The Phoenix test flight would have failed were it not for the intervention of the Enterprise crew
To be painfully blunt, Cochrane was a drunk and mentally unstable. The Phoenix was cobbled together from salvaged parts and a converted nuclear missile. In the ENT episode "Dear Doctor", Archer is adamant that the technologically advanced, peaceful Valakians just don't have the necessary skills to handle warp drive technology. Yet humanity developed it in a post-World War III shanty town built around an abandoned missile silo!

Enter the crew of the Enterprise-E, who are determined to ensure that not only does the Phoenix test flight go off without a hitch, but they also want to make sure that it happens at the exact date and time required to cause first contact with the Vulcans. To this end a bunch of late-24th Century starship engineers swarm over the Phoenix and make sure that it is in perfect working order in time for the historical flight. But this could be seen as a case of a Stable Time Loop and You Already Changed the Past.

The Phoenix does work perfectly, as one would expect given the fact that it received extensive pre-launch service from engineers from 300 years in the future! One is left to wonder if, had the Borg not led the Enterprise on a chase into the past and done enough damage to the launch site to justify sending in engineering teams to work on the Phoenix, whether the actual vessel, as constructed by Cochrane and his followers, would have actually worked, or if it would have succumbed to some mechanical failure. Lily Sloan seemed to be the only person in the whole settlement, including Cochrane himself, who took the ship and the flight seriously. Cochrane appeared to be running on drunken ambivalence and constant prodding from Lily. The actual test flight appeared to have nothing even resembling the usual rigorous procedures of a space launch.

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If the whole Time Travel incident had not occurred, it seems as if odds were good that the Phoenix would not have worked, Cochrane and Sloan would have died during the failed test flight, and first contact with the Vulcans would never have happened.

The Borg weren't just looking to erase the Federation from history when they selected the First Contact date.
Rather, they wanted to kill two birds with one stone: to derail the Federation, and to acquire whatever they could of a technology which, in later eras of Star Trek, would've been entirely suppressed: genetic augmentation. While Khan and his ilk were gone by 2063, records of the research that created them would've still been available for looting, along with thousands of frozen Augment embryos that wouldn't be moved to Cold Station 12 until much later. The Borg already possess cybernetic technology far beyond the Federation's, but Augmentation constitutes an alternative form of "upgrading" they could assimilate, provided they went back to an era when the Augments themselves were no longer an active threat.

The Borg weren't trying to prevent first contact at all
Rather, they were trying to provoke a reaction from the 29th century Starfleet in the hopes of assimilating one of their ships. Their exposure to Voyager might have led to the discovery of their interactions with Captain Braxton, and they saw it as an opportunity to acquire future technologies. So, they attacked the future homeworld of starfleet (which is also the current homeworld of starfleet) in a way that would not immediately be obvious as a lure. They might even have specifically given Picard the insights to destroy the cube, so they'd have an excuse to deploy their time-sphere. Unfortunately for them, the Enterprise followed the borg into the past, which meant that future starfleet didn't need to send a timeship into the past. The queen tried to contact the First Contact-era Borg to disturb the timeline in another way (causing an earlier federation-borg conflict would have significantly changed federation history, which would remove future starfleet) to provoke an intervention, but was succesfully stopped. The remaining drones from 'Regeneration' tried to do so again, but only succeeded in setting up a stable timeloop (in fact, maybe Q deliberately introduced the enterprise to the borg at that point to cause it to become a stable timeloop.)

The Borg Queen forced all the drones aboard the Enterprise to self-destruct before she died
The destruction of the Borg Queen at the climax may have been intended to take out all the drones aboard the Enterprise at the same time, but this is inconsistent with what we later see on Voyager, namely that the death of a Queen doesn't do much to affect the rest of the Borg. And given that back in TNG's run we saw damaged drones self-destructing, it seems likely that the Queen knew as soon as she fell into the plasma coolant that even if she didn't die immediately she wasn't going to be making it out alive, and so sent the self-destruct command to all the drones aboard the Enterprise, thereby killing all the assimilated crewmembers before Picard can try to help them, and thereby at least managing to inflict something of a Pyrrhic Victory on him.

The original-series crew referring to Cochrane as being from Alpha Centauri wasn't a continuity error.
Some years after First Contact, Zephram got so fed up with being hailed as Earth's greatest inventor and the initiator of contact with the Vulcans that he walked away from fame and tried to retire to obscurity back in Montana. Unfortunately for him, Bozeman had grown into such a tourist-trap shrine to his discovery that it didn't offer any escape from notoriety, either. Unwilling to settle anywhere that he'd been "turned into a statue" by his admirers, he eventually overcame his distaste for air/space travel and emigrated to Alpha Centauri - a frontier planet newly colonized by humans, where everyone was too busy founding settlements and taming the wilderness to care whether a newcomer was a celebrity or not - where he spent the remainder of his retirement, only rarely returning to Earth for ceremonial cameos in Enterprise.

Alternatively, there could've been interstellar travel at relativistic speed before and during WWIII.

If humans could travel at about .5 of light speed (theoretically doable IRL from the 1970's with nuclear pulse engines, I believe), that's eight and a half years (on Earth or another stationary point of reference) or seven years and four months (ship time, which, per relativity, would pass at circa 86.60 percent of normal) to travel to or from Proxima Centauri (4.24 light years from Earth). Correct my math if it's off, but I don't think it is.

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Now, First Contact takes place in 2063. There could have been a colony founded in the 1990's, around the time of the Eugenics wars, with semi-regular commerce back and forth until sometime during WWIII, which lasted from 2026-2053. That's plenty of time for Zephram Cochrane to be born on Alpha Centauri and travel to Earth.

Now, this a lot of math and references to explain away a throw-away line from a series that, overall, doesn't have great continuity with its successors. However, consider this theory as part of the following WMG:

Building on the above, Star Trek is set in a timeline that diverged from our own circa 1960-something.

So there's all this attempt to square references to the Eugenics Wars with the way history turned out in real life. I don't get it. Star Trek is perfectly willing to allow multiple timelines even in the course of its own canon. (It's not like the Kelvin timeline was the first time history was changed in canon. What time-travel episode hasn't changed the timeline slightly?) Why can't Star Trek be in a different timeline than our own? We're certainly not on track to have FTL by the 2060's, although WWIII by the late 20's might still be achievable...

So the Eugenics Wars were fought in the open (with nukes and all) in the 1990's, slower-than-light interstellar ships were launching as early as 1975, and the Soviet Union continues existing in some form or another well into the TOS era, as opposed to dissolving in the early 90's. (Why the Soviet Union? There's a throwaway line in TNG, I think. One of the movie-era Starfleet ships they find adrift in space was recorded as being commissioned in the Soviet Union at Baikonur, iirc. Also, Chekov's jingoistic posturing makes a lot more sense if the Soviet Union had existed within his lifetime, perhaps even during TOS.)

The main objection to this theory is that, every time someone in Star Trek travels back to the approximate year the episode/movie was written (AKA, about once per series, barring The Next Generation and Deep Space Nine, and one movie), the world they end up in doesn't really differ that much from that period of our timeline. To me, this isn't much of a problem. The Eugenics Wars could have been going on when Voyager traveled back to the 90's in Future's End (in fact, canon implies that they had just ended,) and we might never know it from what was shown on screen. Refresh my memory: does anyone in The Voyage Home ever say that Earth wasn't sending out slower-than-light interstellar spaceships in the 80's, when the Enterprise bridge crew visited the past to save the whales?

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