Pregnancy depends on proper timing of ovulation & unprotected sex. Brown vaginal discharge
with late period seems to more likely implantation
bleeding or sign of miscarriage
Therefore, you should undergo one blood test
for beta hcg & Trans Vaginal Sonography (TVS) scan to confirm or exclude product of conception if any.
After that, you should consult with your doctor for suggestive measures according to test reports.
Avoid stress, take healthy diet with more vegetables & fruits and maintain genital hygiene properly.
If you need further consultation with me, then you can visit http://www.healthcaremagic.com/doctors/dr-soumen-patra/63326.
Be well & take care.