What Does It Mean To Have Breakouts, Dark Brown Discharge And Nausea After Unprotected Intercourse?

I'm almost sixteen and I am sexually active. I'm on the pill but had to stop it for a few weeks because they didn't come in the mail. My boyfriend and I did have sex the first week I was without them because I forgot I didn't have them since I was so used to taking them. My period was supposed to come two weeks ago in a Sunday. It didn't come so I just started taking my pills that day again. The following Thursday I noticed dark brown discharge which I usually get the last two days of my cycle. I've been having that discharge for a while. It's been nine days that I've had the brown/black discharge, but no period. I'm really scared. I've been having cramps for a few weeks, also. I've also been starting to break out and have been nauseous mostly at night.