Hi. Thanks for your query and an elucidate history. Missing the pill may not cause cramps; The return of Endometriosis can cause pains. But there are other reasons which have to be considered, such as: Ovarian cyst as you have correctly suspected. Salpingitis PID- Pelvis Inflammatory Disease Severe enteritis Appendicitis I would suggest you the following: Take your wife to the Gynecologist who would examine her internally by per-abdominal and per-vaginal examination; this give a clinical diagnosis and to be supplemented by ultrasonography or a CT scan of abdomen. A diagnostic laparoscopy and procedure as needed can help a diagnosis and a proper treatment as well .