The game starts in a forest, and among the trees there are many strange metallic pods. The people in masks seem to be working around them, but in the early game it isn't clear what, if any, significance the pods hold. Later on in the game, however, we see the pods often contain drones (human-shaped creatures that will not act unless directly controlled), and even within the heart of the industrial environments they are still seen connected to trees (although not in all cases). It's possible that these pods are used to "grow" the drones, and that along with the strange slug-like mind-altering creatures seen on the pigs in the farm, organic plant matter is maybe used in the process. The large wheeled containers of plants seen in the final sequence of the game could be further evidence to support this. Maybe the slugs are initially hatched and grown on the pigs, and then after reaching a certain stage of maturity are brought to the forest pods to incubate. The masked workers rounding up people in the forest could actually be seen as "farmers".
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