How do I gather infected resources to go to production?

Infected resources come from harvesting the terrirories (plots) that you occupy in the doomsday event. You have to start with empty plots and then level 1 , then 2 etc.

Empty plots earn a small amount of infected food, the specific resource plots earn thos resources.

Once you have plots occupied you can go to the territory tab in the doomsday event screen and use the harvest option to collect over time.

You then need to have placed one or more of the production facility honor structures around the alliance centers. This allows you to process the infected resources into usable resources and the special materials that you need to upgrade the honor structure buildings.