>>4844525True, but there are interesting things about when that doesn't work.
1. In Type 1 Diabetes, an artificial infection is detected in one location in the body. The immune system focuses on that while the pancreas (or nerve endings to the pancreas, depends on the papers you read and the current info on T1Diabetes)
2. The body is overloaded. Too much to fight, and can't fight it. The body starts to destroy everything and the immune system is weakened and maybe replaced in the process.
3. The "loyalty" of the immune system changes. This happens all the time, particularly with cancers. It is not uncommon to have a cancer inside someone up to the size of a golf ball one time in their life. This is not harmful and is later, when the body recognizes it as an impostor, removes it.
4. War of the immune systems. This can happen in transplants if the genetic information isn't close enough. It ends up with death all over the body, but either the body dies or one is victorious.
I am going along the lines of a primer that modifies the immune system via a heavy infection from a chemical or simple cell. The body fights it, becomes weaker, then the virus it let loose to modify the cells.
It is a story involving post-apocalyptic world + a dab of cyborg + angels, naga, centaurs, biological warfare, a person with tentacles, village-wide experimentation, political morals, biological manufacturing techniques... lots. I have a story board and layout of each section, but i suck at the chit-chat writing.
Generally a world where people who know the technology can change a person into something new.