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I know that the UNSC had use nuclear weapons against the Covenant, but why not chemical or biological warfare, or both? They would've been extremely effective, because none of the aliens (presumably) would've been exposed to the same pathogens as we have been, thus they would have no natural defenses against said pathogens. Anthrax and nerve gas would still do their job against living targets, and (so far as I know) the Covenant don't have any gas masks or counter bio/chemical warfare tactics.

So why not just carpet bomb the Covenant with gas and biological weapons when they land on UNSC planets? I know that would cause massive amounts of damage, but I'd imagine that the UNSC high command would find the consequences of using said weapons insignificant against the threat of extinction.

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    "none of the aliens (presumably) would've been exposed to the same pathogens as we have been, thus they would have no natural defenses against said pathogens" - surely they could equally have no natural vulnerability to said pathogens? – Paul D. Waite Jul 9 '13 at 15:23
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    So you are speculating that: a.) multiple intergalactic species evolving independently in complete isolation will be susceptible to the same bacteria (when there are already species on Earth immune to anthrax) and chemicals as humans, and b.) a federation of species that have mastered space travel do not know how to construct gas masks (if they even need something that clumsy and primitive)? – Lèse majesté Jul 9 '13 at 16:00
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    @Lèsemajesté you can even see some of the Grunts wear some sort of rebreather/gas mask. Quite a few of the other Covenant species wear full helmets that presumably filter the atmosphere or provide an internal breathing environment as they don't all originate from the same environmental atmospheres. – Monty129 Jul 9 '13 at 17:50
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    @Monty129 - indeed, the Grunts must breathe Methane. I don't believe Elites require masks, but the helmets are part of their armor, though they don't appear to be sealed. – The Fallen Jul 11 '13 at 13:52
  • If they were able to develope a pathogen of sorts (the flue for example) they could just inject it into a covie on a ship or something and then let it do its thing, this would be very effective since if the solders could get out unnoticed it could kill from the hundreds to the millions of them, and the unsc can just do it over and over again in various locations with different deseases, it would be very effective in a gorilla war – user42986 Mar 14 '15 at 7:57
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In the second book of the Kilo-Five triology,

Dr. Magnusson finds out about Sangheili food from Jul 'Mdama and acquires some, but only to genetically engineer it and test the results on Jul and some Sangheili livestock which she had also obtained, with future plans to permanently contaminate the Sangheili food supply.

Presumably ONI had indeed been working on bio-weapons during the Human-Covenant war, but failed to produce anything viable before the war ended. They did attempt to experiment using the Flood, as explained in a story from Halo: Evolutions, but that obviously backfired. I haven't seen anything else definitive on the subject relating to the actual Human-Covenant War (and I've read all the Halo novels), but from a thread here, several theories are posited (quoting):

  • You're wondering why we never used biological weapons when the only planets that saw any fighting were UNSC held planets that the UNSC wanted to hold against the Covenant? What is the point of bombing a world with biological weapons making it a lifeless rock essentially for the foreseeable future when the Covenant are trying to do the same? The UNSC would have to evacuate the entire planet before bombing it and the Covenant would most likely evacuate at the same time to start glassing the planet, resulting in biological weapons being useless. The only time it would be useful is if the UNSC managed to locate a Covenant held planet and managed to fire the bio weapons at the planet. Which the UNSC couldn't do as up until the end of the war the UNSC didn't know where any Covenant planet was. Basically, you don't use biological weapons on your own territory as the enemy is not hurt in any appreciable way, all you would be doing is their job for them. The Covenant had no intention of occupying the worlds they attacked, they intended to make them lifeless and to exterminate us.

  • The UNSC rarely took Covenant prisoners. They rarely had the opportunity to do so. The few times they did was to try and extract information and yes, sometimes to use as test subjects. Also, creating biological weapons is complicated and requires a number of things. For example, they'd need to first know what is toxic to the species they're targeting and whether it would also be toxic for humanity

So the big factors seemed to be not knowing if the weapon would backfire on humanity and an unwillingness to destroy planets that they were trying to save.

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    Would have been funny if the covenant captured humans with peanut allergies and made a chemical weapon from peanuts. They just keep getting more uses! – David Starkey Aug 19 '13 at 17:37
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There's no particular reason that the UNSC couldn't have done it - with massively different physiologies, from each other and from humans, it's very likely that various species of Covenant could have been susceptible to agents that are harmless to humans. This would have forced them to wear hazmat/sealed gear on UNSC planets, possibly reducing the advantage of their shields. At least Elites, Jackals, and Grunts have demonstrated sealed-breathing systems in multiple games, and presumably the other members of the Covenant have their own equivalents.

However, humanity took very few prisoners, live or dead (the Covenant would glass any planet they didn't take with a ground assault), and fought mainly a defensive war. There weren't opportunities to attack Covenant civilians, just defend against the fleets and armies. Even if they got enough samples and made a breakthrough to create such an agent, in those situations, chem/bio weapons are of limited effectiveness against space-borne forces.

We saw, in fact, what would have happened if humanity had brought a bioweapon to a Covenant installation with noncombatants - the Flood overran High Charity in hours.

But, there's another reason that we never see the UNSC use these sorts of weapons, one that I think is more compelling: we as humans don't like writing about them. Chemical and biological weapons are so scary that we couch them in terms of Zombies, Vampires, Werewolves, and the like, because the reality is too terrifying. There really isn't a defense against them - witness mustard gas. Witness sarin. Witness white phosphorus. They're so hideously effective, and so very not testerone-fueled manliness, that who really wants to give them to the "good guys" in Halo?

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