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The mechanics of flood infection only appeared during game on Halo 3. And as far as i uderstand, we never have been on a major outbreak where spores are released in enough numbers to infect people by breathing while at the same time have infectable allies around. (In wars we have, but at least not in the main games)
The only one i can think of, is the end of cortana when the arbiter appears. Why Thel is not affected by the spores is something beyond my knowledge, however i can answer why the chief is not affected.
mjolnr armor.
thats it
is a full body armor completely isolated from the outside and it has air filtration, so spores dont get to him, and since it covers his whole body an infection form would need to break it in order to infect him.
getting back to the arbiter, we could assume that he also has never been on a major outbreak for too long.
he fought the savage flood on installation 04 during halo CE but that wasnt a major outbreak (spark even mentions that the flood still havent started to change the atmosphere) and he also fought the flood on installation 05 and the treshold gas mine during halo 2, in the treshold gas mine it was a minor outbreak that had just started, and in installation 05 we never actually get to see a flood hive. Granted, the concept of a flood hive probably didnt existed yet, but the canon works in weird ways, meaning we are looking at a retcon that still hasnt been done.
so my own headcanon is that all available biomass was used to make the gravemind or the hive is far away from the locations of the missions.
in either case, the gravemind is sendind the flood there so there arent much spores in the air.
and high charity on halo 3, he only appears at the end of cortana, so we could assume he arrived not too long ago. So he hasnt breathed many spores.
You die anyways so they might as well have him get infected on screen, it would be cool
usualy the flood prefer infecting weaker creatures because its easier for them to create a new combat form, waste less energy
Lore reason: Because MC never even gets touched by Flood to the point of where that was a possibly.
EXCEPT in one case where, in 'The Flood', he gets ambushed by a lone infection form which actually inserts its tendrils into his spine if i remember. Cortana saves him by vaporising the Flood form by overcharging his shields.