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In Star Trek Enterprise (Regeneration) the Borg assimilate some people, cause havoc and run amok. During all this Phlox gets infected with some nanites and begins to be assimilated. However, he ingeniously develops a method of deactivating all the of nanites in his body, essentially curing himself and preventing his impending oneness with the collective.

In universe, why wouldn't this knowledge still be available and even improved upon, perhaps being turned into some kind of a weapon, by the 24th century? Starfleet knew the Borg were a threat and were out there. They knew they would run into them eventually, and that they were woefully unprepared.

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    I don't think the NX-01 that dealt with the Borg (caused by future events in First Contact) is the same NX-01 that was in the TNG's history (until maybe after First Concact). Temporal mechanics is hard (and a great way to retcon things). Aug 2, 2013 at 1:07
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    @muistooshort: You mean that essentially the entire timeline we watched, spanning all of TOS, TNG, DS9 and VOY, up until First Contact, was deleted already by the ENT episode and presumably played out quite differently? I don't (want to) believe that ... Jul 30, 2023 at 20:27
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    Borg technology advances as well.... Jul 30, 2023 at 22:39
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    @O.R.Mapper Enterprise, ironically, is the only Roddenberry/Berman Trek canon to JJ trek/Kurtzman trek. I use ironic due to ENT's obvious continuity problems with TOS/TNG/DS9's classic trek canon. Like I comedically spit my drink out when I read an interview that DISCO writers had watched Enterprise to make sure they were capturing the feel of classic trek. Jul 30, 2023 at 22:51

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Given that Picard's assimilation was able to be completely reversed (even after a much greater length of time with the Collective - see Best of Both Worlds), it is not clear that this cure was "lost" at all. The Borg threat is not merely that they can assimilate in this way, but that they can quickly overwhelm defenses and take over an entire crew (or even planet). A cure won't help if you have no opportunity to use it.

Perhaps Phlox's initial research into the nanoprobes is what allowed Picard to make a complete recovery in the TNG timeline.

Additionally, it is reasonable to assume that the Borg can adapt their nanoprobes (just as they can adapt their defenses), nullifying any attempt at immunity. The Federation would have perhaps underestimated the Borg's adaptability; perhaps they did design a weapon based on this research, but it was rendered completely ineffective by the TNG timeline. This answer feels a little cheap to me, but I suppose it works for the Borg.

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    I don't think Picard's crew knew anything about the Borg. It seemed like they were a completely new threat. Jan 31, 2012 at 16:04
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    @Wikis You can't expect Picard's crew to be aware of a single, perhaps classified, single event some 200 years in the past. Someone may have made that connection after the fact, but during the first Borg encounter they were rather occupied at the time. Jan 31, 2012 at 16:44
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    @FrankPierce: Actually, it is possible that someone on Picard's crew should have known. A lot of military officers tend to look up the records of previous incarnations of the vessel they serve on, and Archer's and Kirk's must surely have been the most famous ships to bear that name at the time. At the least, you'd have thought Data would have read and remembered those records.
    – Tynam
    Apr 14, 2012 at 23:39
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    @Tynam I doubt it - in The Naked Now, only Riker had any recollection of an event ~100 years prior. 200 years is pushing it for relevance to their era, plus the NX-01 Enterprise wasn't necessarily a previous incarnation - it was from before the Federation was founded.
    – Izkata
    Sep 17, 2012 at 22:42
  • @Izkata: The event being someone showering with their clothes on, and it could be found in the library computer. If something trivial like that is found, shouldn't information about a major threat of unknown origin be much more prominent? Jun 30, 2015 at 5:42
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It's actually explained in Regeneration that, as a Denobulan, Doctor Phlox's metabolism is much more efficient than a human's metabolism, which is why it takes so long to assimilate him; just like Species 8472 who proved impossible to assimilate due to their highly active metabolisms. Moreover, it's heavily implied that the Omicron radiation used to purge the nanoprobes would likely kill a human, and only Phlox, as a Denobulan, could use this method to avoid assimilation.

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I feel a lot of people are forgetting the collective consciousness of the Borg. They are a power based on their size. Remember, in all encounters with the Borg, regeneration is a collective thing, so the more Borg in the collective, the stronger their abilities. So if the Borg had thousands of members, they would be able to adapt, assimilate and repair faster and better in all ways than a few handfuls, especially ones that are using technology from hundreds of years before the Borg's next gen. The way I see it is in Voyager, Seven of Nine says the nanites are programmed to use the tech they encounter. Well, to me, even though the drones were from the future, the nanoprobes are using the current time zone tech, which means they're not as sophisticated and as powerful as they would be 200 years later.

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