No one looked comfortable at the sentencing hearing. Not family and friends who packed the US military courtroom's straight-backed benches. Not the rookie Army prosecutor in stiff dress greens who flushed with every "Your Honor." Not Judge R. Peter Masterton, whose usually animated face was now grave.

And not the convicted deserter – Army medic Agustín Aguayo – on the stand in a US military court in central Germany last March, pleading for understanding.

"I'm sorry for the trouble my conscience has caused my unit," Private 1st Class Aguayo said, his voice thick with emotion. "I tried to obey the rules, but in the end [the problem] was at the very core of my being."

Colonel Masterton, a veteran military judge, stared down at his bench. The defense wanted him to free this man of conscience. The prosecution asked that he put the coward away for two years to show other soldiers that "they are not fools for fulfilling their obligation."

Aguayo craned to face the judge. "When I hear my sergeants talking about slashing people's throats," he said, crying openly, "if I'm not a conscientious objector, what am I when I'm feeling all this pain when people talk about violence?"

Next door in the press room, where reporters crowded to watch the proceedings on bleached, closed-circuit TVs, a soldier guarding the door wiped tears from his face.

• • •

Every war has its deserters, troops who abandon their posts. And every war has its converts to pacifism. The Defense Department reports that 5,361 active-duty service members deserted the US Armed Forces last year; nearly 37,000 since October 2001. In today's all-volunteer force, that means a desertion rate of less than half a percent – much lower than the Vietnam War draft era, when it reached a 1971 high of 7.4 percent. In the past six years, 325 Army soldiers have applied to be recognized as conscientious objectors (COs), soldiers who no longer believe in war; 58 percent were accepted.

Still, Aguayo's story is revealing of the mental battles of these thousands who change their minds during a bloody war – and, arguably, of many who don't.

Struggling to support a young family in the patriotic months after 9/11, Aguayo chose to serve a nation heading into a long fight. War made a man of the naive private – but not in the way his officers intended.

While his struggle to believe in his mission probably resembled that of many young recruits, no one imagined how it would end.

• • •

Aguayo is a small, soft-spoken man, tentative but quick to smile. Born in Guadalajara, Mexico, he immigrated legally to Los Angeles with his parents when he was 4. At 19, he became a citizen and married a girl he'd met at church, the daughter of Guatemalan immigrants. He worked a dead-end bank job; for his twin daughters' sake, he wanted more. So he got second and third jobs and enrolled in community college. At Home Depot, where he worked in the fall of 2002, the radio blared through his shift with Army Reserve ads promising he could stay with his family and get a four-year degree.

On the way to renew his driver's license, Aguayo saw a recruiting station and stopped in. "No, you don't want the Army Reserve," he recalls the recruiter saying, "have a seat." Two weeks later, Aguayo joined the active-duty Army. His wife didn't want him to – the Afghan war had subsided and the Iraq invasion was imminent. "But he was so excited and so sure that the future would hold great things," Helga Aguayo says, that she supported his decision. She recalls asking him what he'd do if he had to go to war. "He kind of laughed and said, 'They train you for that. I'll be a different person.' "

But in basic training at Fort Benning, Ga., Aguayo couldn't adjust like other recruits did. It pained him to march to "Left, right, kill!" and to chant "We are not men. We are beasts." He stumbled out of gas-mask training crying, and wrote to Helga that the sting of the gas made him think of Nazi gas chambers. "The point is for you to learn how to use the mask," he says, "but [the gas] hurts, and I'd never want to hurt anyone like that." He hoped his qualms were normal, that he'd master them.

In August 2003, five months after the US invaded Iraq, Aguayo's unit was sent to a base in Schweinfurt, Germany. There they received orders to deploy to Iraq in the new year. His roommate assured Aguayo that the war was over and they would be peacekeepers. Aguayo, who rarely followed the news, felt better.

Then their training changed. "It wasn't targets anymore. It wasn't about me getting a badge. It wasn't about me getting a pat on the back," he says, "It was about me getting ready to take someone down."

In February 2004, on the eve of his Iraq deployment, Aguayo confided to Helga, who had joined him in Germany with their 8-year-old daughters, that he wasn't willing to kill, even in self-defense. She was alarmed. She searched for help online, and found a story about a marine who had refused to serve in Iraq. They read it together; some of the words were new to them.

"I had never heard the term 'conscientious objector,' which is embarrassing," she says. They Googled it, and called the hot-line number that came up. Volunteers explained the application process, and Aguayo, deploying in two days, hurried one together.

In Iraq a week later, he woke to the sound of shouting. Near his Tikrit aid station, a US military truck with five passengers had hit a roadside bomb. Aguayo zipped two officers up in body bags. His horrified expression caught the attention of a physician's assistant who took him aside. "You have to understand, there is a bigger picture," Aguayo remembers him saying, "God has a bigger plan."

"I couldn't reason like that," Aguayo says. "I thought, 'How can God have anything to do with this?' To me it was ignorance: on our side and on the guys that put the bomb out there."

Aguayo never got used to the routine cruelties of war: The men in US uniform he heard speak lewdly to veiled women, the American squads that cut clotheslines on Fridays while families were at prayer. "When someone sees me on a corner, then sees this guy next to me," he says of these soldiers, "he thinks we're the same."

Despite his misgivings, Aguayo developed a reputation in his unit as a mature presence and a diligent worker. He was promoted to the rank of specialist and recommended for another promotion to noncommissioned officer status, which he refused. Friends who served with him say that although they didn't share his beliefs, they respected his growing pacifism.

For his 12-month tour, Aguayo refused to carry a loaded weapon. His medical duties didn't require one, but dangerous patrols in Saddam Hussein's hometown did. Out of consideration for his beliefs, superiors looked the other way as he hoisted an empty rifle. When he told Helga, she was appalled at the danger he was putting himself – and others – in. "I said: You can't do this. You have a family. You have to come back," she says.

In August 2004, Aguayo's CO application was denied. The decision was divided: Aguayo's company commander and investigating officer called him "absolutely sincere" and said he had a "legitimate concern with being a soldier." The next four levels of command recommended rejection; one called Aguayo's application "an attempt to remedy [the] anxiety all soldiers face during an extended deployment in a combat theater."

Aguayo knew there were other ways out: A friend used illegal drugs to get discharged; others went AWOL. But he hated the idea of breaking the law. So the Aguayos threw themselves into challenging the decision when he returned to Germany in February 2005. Superiors decided that whatever the result, he didn't belong in the Army. A sergeant took him aside and promised to "paper" him out: charge him with enough small defiances to disqualify him from service.

But with only one infraction on record – failing to raise his M-16 in a training exercise – and another pending, his unit got word. They were going back to Iraq.

• Tuesday: A desperate escape, a prison cell, and a political awakening.