Re: Fatal Flaw?
Not knowing anything about the story -- would embedding the memory chip into your protagonist work? He wakes up, disoriented, his neck is sore, and he receives a call -- if he's not at so-and-so by such-and-such -- a small explosive charge, connected to the chip, is triggered and he's dead. Maybe he's just returned from a trip to a foreign country. The "bad" guys don't care how they get the chip out (dead or alive) -- the "good" guy knows the code and how to disarm it.
That said, you could go the route of "District 9" -- just ignore the questions about how alien "power" juice can change the DNA of a human to that of an alien. I still liked the movie -- even with a plot hole so big you could fly a starship cruiser through it.
STANDARD DISCLAIMER: I'm a wannabe, take whatever I write with a huge grain of salt.