Missed pills and brown discharge

Patient: Ive been taking the pill (Alesse) for 2 months now but i missed it on sunday so i took two on monday then i missed it on tuesday so i took two on wednesday. On thursday, i had brown discharge and since then(sunday) its been continuing. I also had unprotected sex during that time but my boyfriend did not cum inside. What is happening? Will it ever stop? do i have to stop taking the pill and restart a new pack? what do i do?Thank you!