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In the Voyager episode Scorpion the crew encounters Species 8472. They learn that the Borg started a war with them, but now the Borg are losing. Seven explains why they are so keen to assimilate 8472:

SEVEN: Species 8472 was more resistant than we anticipated. Their technology is bio-genically engineered. It is superior to that of all species we have previously encountered.

TUVOK: Which is precisely what you wanted.

SEVEN: They are the apex of biological evolution. Their assimilation would have greatly added to our own perfection.

However, the crew is able to create a weapon that proves to be most effective against 8472. They test it successfully and then move on, without giving the Borg the recipe for the weapon, and without being bothered by the Borg:

Captain's Log, Stardate 51003.7. Three days, and no sign of Borg or bio-ships. We appear to be out of danger, but the entire crew is still on edge and so am I. Not even the calm of Master Da Vinci's workshop is enough to ease my mind.

Now the Borg are at war with 8472, they are losing. Even if 8472 is now under the impression that the Borg could fight them and they decide to return to their fluidic space, the Borg will still want to assimilate them and therefore they will need the weapon.

So how come the weapon isn't the highest priority of the Borg? Why not send all available ships after Voyager? Are the Borg... grateful? Do they decide to honor their agreement after all? Or (to me) the most fascinating alternative: do the the Borg decide to make peace with 8472?!

  • @PaulDWaite: Thanks again! – Einer Jun 3 '14 at 13:50
  • -huff- if only they had perhaps we would have been saved from 3 more seasons of Voyager =P – 22nd Century Fza Jun 4 '14 at 3:12
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    @22ndCenturyFza Voyager is a frustrating setback after the space-opera/epos called DS9. But as it is there is no new series of the Star Trek franchise so I'm stuck with the old stuff and reviewed Voyager for the n'th time. So I'm kinda glad they made some more episodes, even though the bulk of them are not worth watching them. – Einer Jun 4 '14 at 6:45
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    @ Einer - ((HI-FIVE)) DS9 was excellent! Have you watched SGU? It's kind of what I wish Voyager had been (probably a little more dark than Trek should be but it really did the 'desperate stuck on the other side of the universe' thing the right way. – 22nd Century Fza Jun 4 '14 at 7:29
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    @22ndCenturyFza I did watch it and I loved Robert Carlyle - it's a crime they canceled it. But they canceled it and left us with an unsatisfying cliffhanger (everyone in in stasis and maybe they will never wake up, and that's it). I agree: The whole atmosphere is way more desperate and plausible: 'We may never get back home again sigh!' – Einer Jun 4 '14 at 7:51
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As per the Memory Alpha page you link to, during the episode, Janeway

...has the Doctor save all of the research regarding the nanoprobes in his holomatrix. She also explains that, if the Borg threaten Voyager in any way, the crew will simply erase The Doctor's program.”

If the Borg knew of this (I haven’t actually seen the episodes) and believed Janeway, then pursing Voyager would have resulted in the only known effective weapon against Species 8472 being lost. Not very productive.

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    The original agreement included that the Borg would escort Voyager. If I were the queen, I'd love to do that and spend some more time in the vicinity of my new favorite toy. Yet I don't think that that's the way the Borg think. They don't wait for an opportunity - either they take what they want and know how to do it, or they don't know and they don't take. To me a satisfying answer, anyhow! – Einer Jun 3 '14 at 14:16
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    I know what you mean. You’d imagine the Borg would try to grab the nanoprobes anyway. But the whole premise of the episode kind of falls apart then — you have to believe the Borg need something from Voyager and can’t just take it, otherwise the whole thing (and probably the rest of the show’s run) makes no sense. (This may give a hint as to why I haven’t watched Voyager.) – Paul D. Waite Jun 3 '14 at 14:31
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    IIRC, this is incorrect. This threat was only in place during the first part of this episode. By the end of the episode, the Borg have this technology themselves. They use it to drive 8472 back into their realm and end the war. We find out later in the episode Hope & Fear, that they also used this tech to assimilate Arturis' people. – BBlake Jun 3 '14 at 16:16
  • @BBlake: When was the handover? When was the data downloaded from the doctor and handed to the borg? I'm not saying you are wrong, but I can't remember that scene... – Einer Jun 3 '14 at 16:28
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    @BBlake If the handover was later, than the thread of the weapon being destroyed if they attack Voyager would still be in place by the end of the episode. And it would still explain why the Borg don't attack... that is: they don't attack that episode of course ;-) But if there was a handover that episode, it would render my question void. – Einer Jun 3 '14 at 17:18
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The immediate threat of Species 8472 is over and the Borg Queen is already planning ahead. She knew that Seven had survived and was now being "assimilated" into the Voyager crew. Her long term goal, as we find out later, is the assimilation of the human race. It was what she was trying to do when she assimilated Picard into Locutus, instead of just another drone. She needed someone who would eventually be able to bridge that gap between Borg and Human. Having failed with Picard, and later with Data, she was now using Seven to become that bridge.

She could have destroyed or assimilated Voyager at any time. But her higher goal was all humanity. For that, she needed Voyager intact and Seven of Nine as part of her crew. This plot is followed more later in episodes Unimatrix Zero, Dark Frontier, & Unity.

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    That is plausible. Yet it means that the assimilation of mankind is more important to the queen than the assimilation of 8472. I mean I feel honored to be considered more even valuable than the "apex of biological evolution", and I'd be proud if the queen feels that way. But yet I'm not convinced that she does. – Einer Jun 3 '14 at 13:48
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    The "apex of biological evolution" was defeated by an invention of the lost-in-space Voyager crew. No help, no reinforcements, no resupply lines, and the ingenuity of Voyager's crew comes up with a solution. You don't think that's an attractive race to assimilate? – Brian S Jun 3 '14 at 14:16
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    @BrianS It is impressive. But the Borg invested hundreds of Cube in this war. The earth is only honored by a mere cube and a sphere. Imagine 100 Cubes on our doorstep: We wouldn't have a chance. We surely are tasty but not but our ingenuity works best with our individuality intact - the queen knows that. If thats what she is after, it's better to keep some of us as science-pets in a cage (maybe the Doctor and Janeway) and go after 8472 additionally. – Einer Jun 3 '14 at 14:29
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    @Einer I can't recall if it was Scorpion, or a later episode, but Seven actually makes the comment (or affirms someone else's speculation maybe?) that, when encountering species whose creativity the Borg wanted to "assimilate", they would in fact leave the species alone until they invented something the Borg wanted -- and then they'd assimilate that, but continue to leave the planet/colonies/etc intact so as to continue to reap the benefits of the individuals' creativity. In other words: Science pets -- who don't even know they're in a cage!! – Kromey Jun 3 '14 at 14:54
  • Unity was a season 3 episode (before Scorpion) about a community that had created their own collective? Don't remember it furthering the plot of the Borg assimilating man-kind. You didn't mean Endgame did you? – Jared Jun 3 '14 at 22:19
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Another thing that hasn't yet been mentioned:

In the very next episode The Gift, Kes' transformation allows her to send voyager 9.5 thousand light years closer to home. I imagine this wouldn't leave much of a trail for the Borg to follow. Even if their Transwarp technology is faster than warp drive, they'd now have a very large area in which to be searching for Voyager...

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    Erm, yes. This is an answer to my question - in it's current state. The question has been subject to some editing and now it's asking about the time after 'Scorpion'. Originally it was intended to be about the end of that episode (and the time before Kes stepped in). Nonetheless you are right though. – Einer Jun 4 '14 at 6:35
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Its an old question but there is a simpler answer

The nano probe technology in no way helped the Borg assimilate 8472, it only killed them. The Borg are not interested in killing them. 8472 were chased out of this galaxy and no longer a threat to the Borg, that's enough for now, so why go after technology to kill something that you may be able to assimilate later

The Borg don't kill the races they are interested in, they want them, but would rather wait until they CAN assimilate them than destroy them. The war was over, 8472 thought the humans were allied with the Borg (they weren't but it was enough to stop the war). 8472 was no threat to the Borg the moment they believed that humans would come to their aid, with this devastating technology. This is shown in a later episode where 8472 says 'the Borg are irrelevant it the humans we need to worry about'

So the simple answer is the weapon was useless to the Borg anyway, they needed to stop the war (which Voyager did) but they didn't want to kill them all, so there is no point in going after Voyager. You don't fire a missile at someone you want to incapacitate for the same reason (when your intention is not to kill). The threat the Humans now posed was enough to stop the war and they thought that the Humans and Borg were allies, so left the Borg alone

The threat of deleting the Doctor had nothing to do with it, as in that same episode the Borg told 7 to assimilate the ship anyway (and risk loosing the data they wanted, all they wanted was to stop the war)- even with that threat in place the Borg still tried to get the tech by force (but only to stop the war, which Voyager did for them by accidentally showing 8472 that they will side with the Borg). That is the whole story line of why 8472 were planning an invasion of Earth if needed (Voy: In the Flesh). They feared the Humans would come to the Borgs rescue and left the Borg alone because of that

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