Equip the "EngyChng" (I think it's called that, it's meant to be Energy Change) Navi Customizer block. It's the same one you used to turn Fire Element Battle Chips into fire to burn things during the PlantMan scenario. Use it with Water Element Chips and it creates a blast of water that puts out the fires. There's A LOT of fires to put out though, so if you don't have a big stock of Water Chips, if would be a good idea to equip the "Fish" Navi Customizer block as well, to draw out Water viruses to get their Water Chips.