I interpret those lines as showing that whatever outside influences ("thunder" and "rain") might hinder the relationship the song is referencing, they should be discounted as unimportant ("fool's gold"), trivial, terminal ("warring"-- therefore eventually ending itself). What do you think? Perhaps they are allusions to other poetry, movies, stories, literature, or something entirely personal to Chris (or another band member) as well. Also, this is probably my favorite song on the album. It reminds me of the pop punk stuff I was into when I was in Jr. High... in a good way!