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>Why Bane didn't just tortured Dr. Pavel instead of making an overcomplicated plan?
(see image)
>Why Bane believed in CIA when he said they expected only 1 of us in the flight plan, but clearly saw he wasn't killing anyone, neither throwing them out of the airplane?
Bane knew that people investigating the plane crash outside of the CIA would notice the discrepancy in number of people on board (the flight plan versus the body count). Bane thought that, should CIA survive the crash (Bane knew CIA was an expert in surviving such extreme situations), he would have to leave one of his men behind to stand in for CIA as Bane did not want anyone thinking that, again, if CIA survived, that he could still be alive. This is because Bane knew that CIA's body missing would raise questions that would risk the success of the master plan.
>Why they made blood transfusion when tooth/marrow cells are the ones collected for DNA analysis?
There are four possible explanations:
(1) Bane wanted Pavel confused, afraid, and stressed. A blood transfusion in the middle of what was happening would be a highly stressful situation. This is to assert dominance.
(2) Bane knew Pavel would have questioned how the outside world would think that Pavel was dead. This for-show precaution was not for the official "investigators," who would've known the body was not Pavel's yet reported it so (Pavel wouldn't know this).
(3) Bane is an unreliable narrator and only said that he made precautions to make people think that Pavel was really dead (Nolan interprets Bane's story as a blood transfusion). What many other things are false or otherwise different from reality is unknown. The ridiculousness and complexity of the plan make me think that the true method of abducting Pavel was by use of a highly advanced and top secret aircraft with tractor beam capabilites, which Bane obviously could not speak of to whoever he is telling this part of the story to.
(4) Lazy writing
>Why Bane and Dr. Pavel stayed outside for so long instead of going inside the bigger plane with all the other hired guns?
https://www.youtube.com/watch?v=PErEsNhDmo8
There is a cut for time at about 0:14 to 0:15. Thus, the system takes a bit of time.
>Why CIA didn't checked the handcuffs or used his own handcuffs/legcuffs as it's default procedure when bringing prisoners to an aircraft?
Maybe he did. Bane is just strong enough to break them (remember that they are plastic, not metal).
>Why the pilot didn't alerted they were being hijacked and their situation? At least the black-box would have the registry of what happened if the radio wasn't working.
There are two possible explanations:
(1) The CIA made sure that the plane's instruments were not working properly in that aspect. If they had, then the plan would have not worked (the pilots would have used their better judgement and evade).
(2) The C-130 Hercules had special jamming equipment onboard. Or rather, in corroboration with the 'unreliable narrator' aspect, the C-130 was actually a highly advanced and top secret aircraft with tractor beam capabilites.
>How the plane fuselage is so fragile to allow being penetrated by hand with pins, but so strong to hold all the plane in 2 pins without tearing them apart?
As mentioned twice above, it could be that the small plane either had special fixtures inside to lock into place with the pins (or the outer layer was otherwise purposefully weak) and the paratroopers were utilizing advanced prototype technology. Or the 'unreliable narrator' aspect persists and the small plane was attacked by a highly advanced and top secret aircraft with tractor beam capabilites.