I tried to capture this concept in the Fan Fic Bombshell.
Where although the vilian was killed in a plane crash, a number of interested parties were
a) Trying to keep it a secret
Trying to recover a weapon the villian was carrying
Their reasons for doing this would also set up a double reason for the actions.
I recall also the Graig Thomas novel "Rat Trap"
Where the villian escapes, and is being pursued in oredr to hand him over to an organisation that were conducting a terrorist activity to ensure his release.
It can be done.
We also have the opportunity to use Twins; where one can be publicly killed, thus the element of suprise is retained.
This could be linked in with the supernatural element in some way.