(See Corrections & Amplifications item below.)

SANGIN, Afghanistan—They say there are no atheists in foxholes. There's one on the front lines here, though, and the chaplain isn't thrilled about it.

Navy Chaplain Terry Moran is steeped in the Bible and believes all of it. His assistant, Religious Programs Specialist 2nd Class Philip Chute, is steeped in the Bible and having none of it.

Together they roam this town in Taliban country, comforting the grunts while crossing swords with each other over everything from the power of angels to the wisdom of standing in clear view of enemy snipers. Lt. Moran, 48 years old, preaches about divine protection while 25-year-old RP2 Chute covers the chaplain's back and wishes he were more attentive to the dangers of the here and now.

It's a match made in, well, the Pentagon.

"He trusts God to keep him safe," says RP2 Chute. "And I'm here just in case that doesn't work out."

Prayer on Foot Patrol More photos and interactive graphics

The 460 Army, Navy and Air Force chaplains deployed to Iraq and Afghanistan are prohibited from carrying weapons, counting on their assistants and the troops around them for protection. It can be a perilous calling. On Monday, Chaplain Dale Goetz, 43, of White, S.D., and four other soldiers were killed by a roadside bomb near Kandahar. Capt. Goetz is the first Army chaplain killed in action since the Vietnam War.

Army chaplains represent 130 religions and denominations, including Catholicism, Judaism, Islam and Buddhism. The military says it's common for assistants to be of different faiths from the chaplains they support, or of no faith at all.

"They don't have to be religious," says retired Navy Capt. Randy Cash, who served 30 years in the Chaplain Corps and now is its historian. "They have to be able to shoot straight."

In the case of Chaplain Moran and RP2 Chute, their theological paths diverged long before their career paths joined. Terry Moran grew up in Spokane, Wash., a Seventh-Day Adventist, a denomination that believes the Sabbath should be on Saturday, not Sunday.

Though he admits to some youthful indiscretions and flirted briefly with the lure of dentistry, by the age of 15 he was feeling the pull of the ministry. A minister spoke at his high school and read a passage from the Book of Revelation: "Behold I stand at the door and knock. If any man hear My voice and open the door, I will come in to him and sup with him and he with Me."

In the audience, Lt. Moran "felt the spiritual become real." Two years later, in 1978, the same minister was back urging students to join the clergy. This time Lt. Moran took him up on it, becoming a student missionary in Indonesia, then studying theology at Walla Walla College. He preached at churches and counseled in hospitals. At the age of 39, just prior to the Sept. 11 attacks, he heard there was a shortage of Navy chaplains and signed up.

After several noncombat jobs, he volunteered to minister to the Marine infantry, knowing that such an assignment would likely mean he'd end up in Iraq or Afghanistan. "I needed another deployment in order to stay competitive with my peers," he says.

He drew Third Battalion, Seventh Marine Regiment, a unit headed for Afghanistan's violent Helmand Province. The Marine Corps is a Naval service, and Navy chaplains minister to Marines.

Lt. Moran takes the Bible at its word, rejects the evolution of species and believes the Earth to be 6,000 years old. He carries a large Bible with him into the combat zone, while RP2 Chute totes writings of Richard Dawkins, the evolutionary biologist and fierce critic of the notion that God designed the universe.

Philip Chute was raised a devout Baptist in Nova Scotia and moved to Greenville, S.C., as a teen. His avid reading of the Bible, however, weakened his belief that fact lay behind faith. Soon he was a "full-blown atheist," he says.

He "wasted" a few years after graduating from high school, then joined the Navy. As a Canadian citizen at that time, he found the interesting career fields were closed to him, including his top choice of nuclear-submarine technician. (He became a U.S. citizen in 2009.)

Religious programs specialist sounded better than cook. He rose to the rank of RP2, the equivalent of an Army sergeant, and worked with three other chaplains before he was paired with Lt. Moran late last year.

Soon after they were assigned to work together, they had the inevitable discussion about RP2 Chute's beliefs.

At first the chaplain got the sense RP2 Chute was agnostic. "I can work with that," Lt. Moran recalls thinking.

But a few days later RP2 Chute dropped the A bomb: He was an atheist.

Appalled, Lt. Moran contacted his fellow chaplains. He says he was simply seeking counsel about whether atheists can really be chaplain's assistants. RP2 Chute is convinced Lt. Moran was trying to trade him in for a believer.

RP2 Chute was senior among Lt. Moran's possible assistants. More importantly, he already had two combat tours under his belt, while Lt. Moran hadn't yet seen a bullet fly. In the end, Lt. Moran says, he chose experience over faith.

"We're here for security," says RP2 Chute. "We're not junior chaplains."

The theological differences between Messrs. Moran and Chute have practical ramifications, though, visible during a recent foot patrol in Sangin, a farm town of 20,000 where the Musa Qala and Helmand rivers meet in the heart of Taliban country. The chaplain's aim was to link up with a platoon from Lima Co. that had been fighting for days and provide the Marines spiritual resupply.

Sangin is crisscrossed with irrigation ditches. At one wide canal, Marine engineers had erected a metal bridge to allow the troops to penetrate towards the Helmand River and slice through Taliban strongholds. The Taliban figured that out, though, and an insurgent sniper had recently wounded two Marines at the bridge.

It was a spot that made the Marines nervous.

"Hey, sir, don't get out of the vehicle until I lay down a sniper screen," Gunnery Sgt. Mark Shawhan, an agnostic with a suspicion of organized religion, instructed Chaplain Moran before the patrol. "That's where he's been getting us, and when you cross the bridge—RUN."

Lt. Moran wasn't troubled. "I believe the Lord is going to protect us," he said. But he wondered aloud whether to finish his Meal, Ready-to-Eat packaged lunch before heading to the armored vehicle.

Gunny Shawhan shook his head in disbelief.

When their turn came, the chaplain and his assistant bolted across the bridge and pivoted into a cornfield, where the minister stood upright. RP2 Chute shouted at Lt. Moran to get down. "Take a knee," he yelled.

The patrol zigzagged through fields and waded through ditches, the only sounds the rustling of corn leaves, the muted crackle of a radio and the distant thup-thup of a helicopter flying sentry above.

During a pause to allow the minesweepers to check for booby-traps on the path ahead, the chaplain, wearing his prescription eyeglasses instead of anti-shrapnel goggles, sat down on the bank of an irrigation ditch, dropped his backpack on the ground and snapped a few pictures. RP2 Chute grimaced when he noticed. Insurgents have seeded the entire town with powerful explosives, and Marines step in the exact footprints of the man ahead to minimize the risk.

Lt. Moran says he follows the Marines' safety instruction and wears a helmet, despite his confidence in the divine. But the way he glides blithely through battle is a constant source of worry for his assistant.

"All my training and experience doesn't always help when the man I'm protecting isn't afraid of being hurt," says RP2 Chute.

The patrol stopped at a bombed-out house, where the men from 2nd Platoon were camped out, their fingers black with dirt and faces etched with exhaustion. One Marine asked the chaplain if he'd offer a quick service.

Lt. Moran happily agreed and laid out napkin-sized squares of fabric decorated with the small red-and-blue handprints of children—"prayer squares" sent by a church in Louisa, Va. The children prayed over the fabric, the chaplain told the Marines. "You can put them on your head, and you'll know you've been prayed over," he said, flopping one onto his own head like a newspaper in the rain.

He laid out a selection of religious books: The New International Version of the Bible in desert camouflage. A book called Freedom from Fear. Two books promoted the protective powers of the 91st Psalm.

"Thou shalt not be afraid for the terror by night; nor for the arrow that flieth by day; nor for the pestilence that walketh in darkness; nor for the destruction that wasteth at noonday," the psalm tells believers. "A thousand shall fall at thy side, and ten thousand at thy right hand; but it shall not come nigh thee."

Lt. Moran told Bible stories about angels, but met with silence when he asked the Marines to relate their favorite angel stories. "Even now, where we are, I believe there are angels present," he said.

The chaplain tried to lead the men in a rousing rendition of the Battle Hymn of the Republic, but forgot the words after "Mine eyes have seen the glory of the coming of the Lord," and had to resort to "lala-lala" to fill in the blanks.

But the men sang Amazing Grace enthusiastically and thanked the chaplain warmly for providing a few minutes of relief.

"Everybody made their deal with God before they came," said Lance Cpl. Justin Blaschke, a 21-year-old non-denominational Christian from Woodsboro, Texas.

RP2 Chute looked on, his impassiveness masking his disdain for talk of angels. "It's frustrating to listen to him tell people things I know not to be true, but I know it's not my place to get involved when people come to him for help," he said later.

There are times, however, when RP2 Chute feels he has to intervene and looses his own ample arsenal of biblical references, dredged up from his Baptist boyhood and doubting teenage years.

In August, the pair visited India Co. in dug-in positions on a ridge line overlooking the Helmand River. The company commander asked the chaplain to visit every foxhole. Lt. Moran did so, spending four hours in the mortar pit, fielding the Marines' questions about the End Times.

The chaplain was struck both by RP2 Chute's command of the Book of Revelation, and his refusal to take it seriously. "He's familiar with the Christian doctrine, but he chooses not to believe it," says the chaplain, a slender-faced, soft-spoken man with a fringe of gray in his black hair. "That's what I find puzzling."

On a visit to Kilo Co., a Marine asked for a biblical ruling on tattoos. Lt. Moran said the Book of Leviticus bans them. RP2 Chute disagreed. Leviticus, he said, says people shouldn't get tattoos to mourn the dead.

"I don't believe as Chaplain Moran believes," RP2 Chute often tells the Marines during these visits.

At the end of the foot patrol in Sangin, the Marines sprinted back over the metal bridge and jumped into the armored vehicles that waited on the far side. Lt. Moran crossed and then stood for many long seconds in the open, clearly visible from the compounds where the Marines suspected the insurgent sniper had his nest.

On the near side of the bridge, Gunny Shawhan got out of his own vehicle to yell at the chaplain to take cover, but Lt. Moran didn't seem to hear over the noise of the engines. "Tell the [expletive] chaplain to get behind the goddamn vehicle," Gunny Shawhan yelled into the radio.

"Like bullets aren't going to kill the goddamn chaplain," he muttered to the men near him.

RP2 Chute hustled Lt. Moran to safety behind the armor plating.

Later, Lt. Moran explained that he had been unsure which vehicle he was supposed to ride in. But his serenity had a deeper explanation.

"No matter what situation you find yourself in on planet Earth, God will protect you," he said after the patrol returned safely to base. "All He asks is that you trust and believe what He says. So, if I find myself in a combat situation, His promise of protection is still valid."

Corrections & Amplifications

A photo caption accompanying an earlier version of this article incorrectly identified Religious Programs Specialist 2nd Class Philip Chute as Terry Chute.

Write to Michael M. Phillips at michael.phillips@wsj.com