Jason Bourne, from The Bourne Identity and The Bourne Supremacy often experiences headaches due to something he went through to become the way he is.
What exactly did he go through to get these headaches? Is there an in-universe explanation (perhaps from the books, or in The Bourne Ultimatum) for this?
From The Bourne Supremacy:
Pamela You'd been working at Treadstone for three years, and your cover at the time was what?
Nicky That I was an American student in Paris.
Pamela And what exactly did your job with Treadstone in Paris consist of?
Nicky I had two responsibilities. One was to coordinate logistical operations. The other was to monitor the health of the agents.
Pamela Health, meaning what?
Nicky Their mental health. Because of what they had been through, they were prone to a variety of problems.
Pamela What kind?
Nicky Depression, anger, compulsive behaviors. They had physical symptoms. Headaches, sensitivity to light.
Nicky Before Bourne? No.
From The Bourne Identity, we know that the symptoms affect more than just Jason Bourne:
The Professor Do you get the headaches?
The Professor I get such bad headaches. You know at night when you're driving a car? I don't know, something to do with the headlights.