I'm 21 years old, sexually active, I've never had a regular period, and I'm not on any birth control.

The last time I had my period was in the middle of April (16-20th), Today is August 2, making it 3.5 months since my last menstrual cycle.

Two nights ago (July 31) I was having intercourse when my partner informs me that it appears my period has just started. I was happy to hear this since it has been a while.

I had taken a pregnancy test 6 days ago, the 27th, a week before that, the 20th of July, and the 16th of May all results negative.

Since the 31st of July there has been very little blood and it is very light. I noticed I have a very unpleasant smell accompanied by light brown discharge.

What's going on with my body?

I think you should, quite seriously, see a doctor regarding your health issue (and the odour accompanying it). We can't diagnose on the Internet.

Odor can well be some type of infection, with the discharge, but there are 100s of reasons for no period or irregular cycles.