@maxdancona,
It could be said, metaphorically, that the body "fights fire with fire". And sometimes it over-reacts, or fires at the wrong things, hence auto-immune diseases.
I know a bit about it because my wife had an hepatitis once, and they couldn't find the reason. They ran hundreds of tests, even an MRI, found nothing wrong, no bug, but a high level of immune reaction. She got better after 2 weeks. The leading hypothesis in the end was an auto-immune reaction triggered by the take of 1 g. of paracetamol the day before it started. The docs could prove she was allergic to it, unbeknown to her. The liver processes whatever molecule the body wants to get rid of, and could have 'stored' a good amount of that paracetamol intake...