Was Nakasugi a marionette the entire time? Other options are: she's been modified into one (like a cyborg) or her memories are being uploaded from her comatose body to a marionette's.
@Redwaterflowing - I don’t think it matters which theory is correct. All I know is, if Tsutomu and Birdy find out, they’re going to go berserk again, like at the lab.