You could be suffering from PCOS or something so since you've missed 3 cycles I would see a doctor. The brown could just be a sign that your period is about to show, but still see a doctor to see what's delaying it for 3 months.
I went 4 months without a period. I bled heavy, then heavy with clots. Towards the end it was brown many days. I actually bled for 28 days. My uterus was thick, an ultasound showed that. I had a biopsy and everything turned out to be normal. How old are you? I suggest you do the colposcopy. Will ease your mind one way or the other. I'll be praying for ya.