This is purely my conjecture based on my readings. The literature refers to peritoneal endometriosis, ovarian endometriosis, and deep infiltrating endometriosis. Current theory points to defects when our pelvic organs are developed (Mullerianosis) that leave stem cells in the wrong place. This might also explain why other mullerian disorders such as adenomyosis are frequently seen in endometriosis patients as well. These stem cells are acted upon by hormones (puberty) to develop as glands and stroma and begin the process of making nerves and blood vessels to support itself - as any good stem cell should. However that tissue should not be in those wrong sites and an inflammatory response happens. Factors from the environment (food, physical activity, stress, etc) play a role in presentation of illness. This is why diet etc might affect symptoms but will not rid the person of the lesions. The different locations of stem cells left behind might influence how they are acted upon by hormones and affect their presentation and the ability to extract them all (trying to spare the ovarian tissue for fertility). https://www.hindawi.com/journals/ogi/2013/527041/abs/
The literature also refers to different stages of the lesions based on color - clear, white, tan, red, black. The different stage can produce different effects on the amount of pain and inflammation it causes.