When brains go wild

Defense mechanisms serve a purpose. Mostly survival, some protection against more harm. Or something. They react fast, since well standing in front of speeding truck/wild elephant for too long won't keep you alive or safe. I know that repeating is the way to create a shortcut or pattern that is easily accessible (ya, commercials know that too!) and that your brain can either think too long that a mechanism serves that purpose or has some hidden agenda about what benefits you, I just don't see how that relates to physical pain.
When pain occurs your body/brain tries to tell you something is wrong. Nothing is wrong now (or so I believe), yet I'm in pain. I know that I won't be dragged out of bed in the middle of the night, I know I won't be smacked silly for something I don't understand was wrong. I'm fine my brain doesn't know that still. But why pain. What is my brain trying to tell me.
I know I will feel shitty whenever I dig into my past too much, but it won't kill me really. Since thoughts cannot do that. Not sure yet if digging into it will change the future, but I think I concluded that that was about the only thing I hadn't done so far to fix certain issues, so why does my brain not agree on that. Since I'm concluding it doesn't since it's sending random pain-messages all over. What would be worse than physical pain here. Or did my brain just go nuts on its own level.
What is this hardcoded thing. I know my brain doesn't like me telling certain things, since it freezes and removes the bridge between thoughts and words. But I can bypass that by just describing those things differently. And it makes sense my brain blocking that. Wasn't wise to talk about things, since that could bring pain. Still that doesn't seem to relate to the pain now.