Surely the machines would have the technology to clean the skies? Can't the machines make a special sentinel designed to filter air, or even simpler than that, simply suck in and compress the smoke, depositing it in solid form into various solid smoke waste dumps all over the world?
Well, remember how much electricity those black clouds store. We see lightning flashes unlike any lightning storm natural weather produces, probably fueled by the fact that all of the sun's heat and light energy is 100% absorbed by the clouds. Given this intense electrical storm, no powered machine would be able to penetrate the clouds for any extended period of time without surely being disabled by a lightning strike. In M3, we see that sentinels are quickly disabled by this lightning, not to mention the Logos ship itself is disabled.
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