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.
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.