While Rogers and Romanoff are in the secret S.H.I.E.L.D. bunker in New Jersey, Zola reveals that Hydra has persisted for decades by infiltrating S.H.I.E.L.D. This casts Hydra as truly resilient and sinister organization with the goal of corrupting and replacing their opponent. Zola also boasts about Hydra's end-game strategy to fully supplant S.H.I.E.L.D. during the deployment of the "next-gen" helicarriers. The pinnacale of the subversion is Zola's "Insight" algorithm for target selection by the helicarriers. The Insight algorithm would allow Hydra to swiftly remove all current & future opposition in a sudden barrage of helicarrier fire. After regrouping and sharing the Zola's soliloquy of hubris, Fury gives "Cap & team" some reprogrammed helicarrier targeting chips.

Fury decides to change the helicarrier's targets:

  • From: Those who exhibit characteristics which oppose Hydra (via the Insight algorithm)

  • To : The very expensive helicarrier assets which would be useful after the coup d'état

Why not employ a more sophisticated retargeting operation:

  • From: Those who exhibit characteristics which oppose Hydra (via the Insight algorithm)

  • To : Those who exhibit characteristics which support Hydra (via the Insight algorithm)

Given Hydra's nefarious ability to "grow two heads, when one is cut off", reversing Hydra's subversion attempt back on themselves seems like an unique opportunity to simultaneously decapitate all of Hydra's heads in a single fell blow, effectively ending their persistent threat.

What in-universe reason does Nick Fury have for not pursuing this more sophisticated response to Hydra's re-emergence and coup d'état attempt?

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    Would it be that easy to detect people who support Hydra? It's a secret organisation that almost no-one knows about whereas those with strong SHIELD affiliations would be very easy to locate. – Valorum Sep 27 '14 at 21:50
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    Perhaps they're worried about the philosophical difficulties around giving a computer program the unrestricted ability to kill based on an algorithm – Valorum Sep 27 '14 at 21:51

There are several related issues here.

The first is that the Insight algorithm can't read minds. It can only analyze data and do statistical prediction of which people match the qualities and characteristics of people who oppose Hydra. Hydra wants to kill them regardless of whether they will actually try to oppose Hydra, merely as a precaution. This sort of "punishment before the crime" isn't really Fury's cup of tea.

Secondly, the algorithm, being a statistical algorithm, will never give you 100% certainty, just a statistical match. In fact, when tweaking such algorithms, it's always a trade-off between false negatives (missing people you want to catch) and false positives (falsely identifying a match). Arnim Zola, not caring much about collateral damage, probably tweaked the algorithm to minimize false negatives, at the cost of more false positives.

It isn't really Fury's way, neither practically or ideologically, to kill millions of people who are either completely innocent (false positive matches on the Insight algorithm) or only potentially guilty (match the characteristics of Hydra supporters, but aren't necessarily Hydra supporters), just to kill Hydra operatives. He speaks several times in the movie about the meaning of freedom, one of which (for him) is not to live in fear that some sky-borne police-machine will kill you before you even commit any crime.

And finally, there's no guarantee that the Insight algorithm can even be reconfigured to find Hydra supporters, especially without Zola.

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    Exactly what I was going to say. On a more practical note regarding why take out the carriers first, when the other team is about to make a touchdown, your first priority should be preventing the touchdown. Fury & company were playing defense at the time, not offense. – Omegacron Sep 29 '14 at 17:40
  • @Omegacron I guess I was discounting the importance of Fury & Romanoff's concurrent operation. I can see how Cap & Falcon would be "playing defense" to ensure the other team's success... – user33229 Oct 2 '14 at 15:55
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    I disagree with this, specifically "This sort of 'punishment before the crime' isn't really Fury's cup of tea". Fury himself specifically says in Captain America: The Winter Soldier that "We are going to neutralize a lot of threats before they happen", to which Captain America replies "I thought the punishement usually came after the crime". Fury clearly has no problem killing people before they do anything wrong. – Dr R Dizzle Jul 17 '15 at 10:07

I think there’s also a practical side to this.

Even if Fury and Hill have remote control of the Helicarriers, those carriers are still full of HYDRA loyals.

A mantra in computer security is that physical access trumps all. This applies here. The HYDRA operatives have direct access to everything on the Helicarriers, including:

  • The fish bubble where the custom server blades are installed
  • The power supply and ammunition for the guns

They have the element of surprise, but somebody just has to review the CCTV footage from that room (or the Winter Soldier has to tell them), and they can remove the custom blades. Oops.

Even if they don’t do that, they have lots of other options: build a new targeting system, patch the old one to lock out Hill/Fury, or even just turn off the guns. Trying to turn the Helicarriers on HYDRA themselves will fail quickly.

Oh, and when they fix it, you’ll need a new plan.

Also worth noting:

Fury/Hill may control the guns, but HYDRA can probably control everything else.

The server chips are described as “targeting blades”, not “magic total control over the entire Helicarrier blades”. We don’t know if she has control over the engines (I would guess not), and if she doesn’t, then HYDRA can just park the Helicarrier over an empty desert until they figure out the targeting thing. Or just fly them around over major cities looking intimidating; that would probably work just as well.

Unless you destroy the carriers, or threaten to destroy them, the custom server blades really don’t pose much of a threat to HYDRA.

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As far as Fury and co. know, there is a very small number of folks that they can count on. If you're up against a massive force with deadly weaponry, the number one priority would have to be eliminating the deadly weaponry. As @alexwlchan notes, the longer those things are still in the air, the longer HYDRA has to turn the tide back in its favor.

There's also the issue of Cap himself, who from his first exposure to Insight registered concern and noted that "the punishment [should come] after the crime". If Fury's plan was to commandeer the Helicarriers and use them against their enemies, Cap would never be on board.

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    Definitely worth considering, especially given how bizarrely eager SHIELD were to suddenly treat their 4 top agents as enemies – Valorum Sep 29 '14 at 14:58

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