Well, not really the brain, but the mind, but point taken...
And yeah, the stresses of living the life of an elite covert operative/assassin; having to ceaselessly infiltrate, assassinate and escape over and over again. As 'Jason Bourne', he was the perfect killing machine, and Conklin and Hirsch treated him as they would a machine, forgetting that there was a person buried somewhere underneath, waiting to snap under all the pressure. In fact, I recall seeing a deleted scene of The Bourne Identity, in which Conklin consults a psychiatrist about Bourne's turning rogue. When Conklin mentions Bourne's perfect track record (even referring to him as a 'unit'), the psychiatrist remarks about how even machines tend to break down if they're overused. She then goes on to mention the behavior modification. So yeah, whatever Treadstone put him through was steadily breaking him down from the inside, and what he experianced on the Wombosi op was the last straw.
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