How do you harvest infected materials in the doomsday event?

Occupy the infected plots starting with very low level plots near your 1st alliance center. The more you can occupy the more you can earn. Once you have 1 or more go to the Doomsday conquest event menu (world map view and tap the doomsday icon on the upper right).

In the Territory section you can see what plots you have and then use the 'Harvest' button at the bottom to collect the infected resources. Do this periodically to keep getting them.

You then need to go to the Honor structures section and use the processing plant building to process the resources to remove the infection.