Given the data you reported (missed the last three menstrual periods, slight brown mucus discharge for approximately six weeks, negative pregnancy test), it is possible that you might be experiencing metrorhagia.
Metrorhagia is an unexplained uterine bleeding separate from the menstrual bleeding. There might be several causes for uterine bleeding outside of a menstrual period including: fibroids, cervical polyps, or a hormonal imblance.
A hormonal imbalance is highly likely to be the cause for your condition, given the fact that you also missed three menstrual periods. When there is no menstrual period for a longer period, the inner lining of the uterus might thicken and the first menstrual period afterwards might be accompanied with pretty heavy bleeding. In your case, this is replaced with a brown discharge.
You might want to visit a gynecologist for a physical examination and hormonal laboratory tests. An additional examination (ultrasound scan, for example) might be needed to try to detect the cause for the hormonal imbalance, if one is found. You might be advised to take hormone-containing medications in order to try to restore the normal hormone production.
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