Here's a little explanation of how that misplaced tissue is influenced:
So you have this misplaced tissue sittin' there, just waiting around. Many things influence how it behaves. Estrogen makes it become like the Hulk- it doesn't replicate, just gets bigger and angrier.
Through complicated processes, the increased estrogen B receptors can make the tissue less responsive to progesterone (which would calm it down a bit- this may be why some women don't respond to progesterone driven drugs). So more estrogen=more tissue activation=more symptoms. The tissue can also have its own nerves (unmylenated sensory C nerves) and blood vessels- after all it needs some nourishment! Endo is a chronic , INFLAMMATORY disease, so all these immune cells come to party (remember the MIT study ID'd 13 macrophages in endo patients), they bring along the cytokines and they just party on down (causing pain, scarring, overall unwell feelings). As the cycle of inflammation, pain, endocrine alterations continues, you may see more far reaching consequences, like pelvic floor muscle spasms, bowel symptoms, bladder irritation, etc. Then you add in that when we don't feel well we may not eat as well, be as active, then everything continues to feel worse. The longer chronic pain continues then the more speedy and strong the pain nerve signals get (central sensitization), and the harder it is to control. Some will try to treat endo by lowering the estrogen in the body; however estrogen protects the heart, brain, bones, and metabolism, so lowering it in the long term can be detrimental to our overall health. (They've even shown how removing endo can result in lowered heart risk! "Surgical treatment of endometriosis leads to endothelial function improvement, resulting in reduction of cardiovascular risk." http://m.humrep.oxfordjournals.org/content/29/6/1205) This is why excision of all the endometriosis is being strongly advocated these days. http://endocomprehensive.blogspot.com/2014/07/why-excision-is-recommended.html