I'm 18 years old, I missed my period for 3 weeks, but when I finally started my period it was a lot shorter, lighter and it was (for the first time ever) brown and I also had brown discharge while I was still on my period. I have been with my boyfriend for two years and have been sexually active for a year now. We don't use condoms or anything for that matter and I have checked myself for STDs and infections already about 3 months ago so I know I can't have anything or so I hope since I am in monogamous relationship.

Since you aren't using any birth control, the odds go up considerably that pregnancy will happen sooner or later. Many women do find they have some unusual bleeding, sometimes thinking it is their period, in early pregnancy.
Since your period was off, try a pregnancy test.