i think lighthing rods have higher priority, i just got lucky and zap the UFO by accident. (i used 2 lightning) . I dont know what will happen if i zap them over the ocean though.
So i have played again and able to easily zap the UFO, just use the thunderstorm near the UFO and if you zap the UFO over the ocean they will search a land so they won't fall into the ocean. Also alien is the source of plutonium. (find how by yourself)
