Hi, and thanks for your query on eHealth forum!
A dark discharge from vagina can be due to a foreign body (like a condom or tempon left behind) or due to cervical cancer or dysplasia, fibroids in uterus, endometriosis, or due to a STD or fungal infection. You will need pregnancy test, ultrasound, STD panel and PAP smear for confirmed diagnosis.
If your PAPs have been negative, then a complete STD panel should be done. Other causes investigated. Bacterial vaginosis treated with complete metronidazole course. Possibility of fungal infection looked into.
In all probability you will have a combination of above mentioned causes. Please also check for diabetes as this can cause these infections to persist. Please discuss this with your gynecologist. Hope this helps. Take care!