It's only tangentially related, but nanomachines were also used to explain things about MGS's politics and psychologies. It's not just that it ruined the supernatural stuff, but the bigger themes about people/society/humanity's motivations for doing things was conveniently glued together with nanomachine mind control.
Please explain. Nanomachines on society and military groups didn't become a political and social issue up until MGS4's timeframe.
And please also explained all the supernatural things it ruined.