No segundo livro da triologia Kilo-Five,
Presumivelmente, a ONI de fato estava trabalhando em armas biológicas durante a guerra do Pacto Humano, mas não conseguiu produzir nada viável antes do fim da guerra. Eles tentaram experimentar usando o Flood, como explicado em uma história do Halo: Evolutions, mas isso obviamente saiu pela culatra. Eu não vi nada mais definitivo sobre o assunto relacionado à Guerra Humano-Aliança (e eu li todos os romances de Halo), mas a partir de um tópico here , várias teorias são colocadas (citando):
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.
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
Assim, os grandes fatores pareciam não saber se a arma seria contra-atacar e a falta de vontade de destruir os planetas que eles estavam tentando salvar.