Why does Bourne get headaches?

Question

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.

Pamela Amnesia?

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?

Bourne Yeah

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.

Answer 1

In her book Robert Ludlum: A Critical Companion, Gina MacDonald draws from The Diagnostic and Statistical Manual of the American Psychiatric Association to discuss author Ludlum’s development of the causes and symptoms of Webb/Bourne’s ailments (p 134-135).

Bourne is the deadly alter ego that Webb assumed to survive the jungle warfare in Vietnam and Cambodia as a member of the Medusa Brigade; in times of stress this alter ego surfaces and the gentle Webb recedes. Unfortunately, Webb will never rid himself of the results of his initial trauma unless he can destroy the cause of retraumatization, specifically, the Jackal. The series explores Bourne’s progression: amnesia and a divided personality resulting from debilitating psychological responses to trauma, then retraumatization, treatment, and gradual progress toward normality, followed by retraumatization, and a final working out of conflict that may result in a reintegrated, whole personality…

Ludlum, drawing on the expertise of relatives in the medical profession, provides plentiful details about causes, symptoms, and retraumatization…

Post-Traumatic Stress Disorder (PTSD) [is] a constellation of characteristic symptoms that develop following a psychologically traumatic event… the immediate systematic responses include heart palpitations or tachycardia, cardiac uneasiness or pain, headaches, giddiness, dimness of vision, and general neurological upselt (exaggerated respiration, dilation of arteries, increased generation of adrenalin). The long-term effects include deep anxiety, depression, hysteria, dissociative reaction, depersonalization, neurasthenia, intense psychological distress when exposed to events resembling the initial trauma event,…intrusive thoughts, flashbacks, and nightmares. There may be a feeling of detachment or estrangement from others, difficulty sleeping, persistent irritability or anger, hypervigilance, exaggerated startle response, guilt, episodes of terror or panic, difficulties making decisions, and a feeling that one’s personality has changed. These are all effects that Webb/Bourne experiences at one time or another in the series.

So, the short answer is PTSD.

Answer 2

The Treadstone project took individuals (like David Webb - who would become Jason Bourne) and used brainwashing techniques/ behavior-modification programs to break them down and rebuild them (stripping away their morality or hesitancy to kill) as ultimate assassins. The modification had chronic physiological effects such as headaches and light sensitivity. This was covered more thoroughly in the books that the movies were based on.