I personally think it's about an addiction to prescription drugs and maybe illegal as well. I know Gerard has had a past that involved an addiction to anti-depressants and being an alcoholic. He's also had thoughts of suicide. In comes "the Hotel Bella Muerte" and "And for the last night I lie, can I lie with you", meaning he wants to die peacefully in the arms of the one he loves. And by saying "she wants it all to come down this time," he means the drugs are taking over, making him want to die. But I don't know, that's just how I see it.