This is about lead singer Chino Moreno's wife, and how from the moment he saw her he wanted to be with her. He tracked her down and no one could take his mind off of her. The line, "Cause you're my girl and that's all right, if you sting me I won't mind" is saying she could've done practically anything to him and it wouldn't have phased him because he was in love. "We'll stop to rest on the moon and we'll make fire, I'll steal a carcass for you then feed off the virus" means he would do anything for her - even die for her. The song goes through the stages of their relationship. In the beginning, they were the bomb couple and no one could bring them down and now there isn't much left anymore. "Now we're all the virus" means that it all went to hell and he doesn't know what to do anymore. This man's love for his partner is so great he doesn't care about how badly she hurts him. She makes him feel good and even though she "stings" he doesn't care. In a way, he's addicted to her. The pain is nothing in comparison to the amazing feeling he gets when he's with her.
The girl in the song is his "Prescription Queen" because of all the drugs she has to take because of her illness. "Rx" stands for "prescription."
Suggestion credit: Tim - Pittsburgh, PA, for above 2