In an ornate chapel at the U.S. Naval Academy in Annapolis, just above the crypt bearing the remains of John Paul Jones, Elmo R. Zumwalt Jr. was remembered during a memorial service yesterday afternoon as the conscience of the Navy.

Zumwalt, the former chief of naval operations who led a revolution in the way the Navy treats its sailors, died Jan. 2 at age 79.

President Clinton escorted Zumwalt's wife, Mouza, into the chapel. Clinton recalled he last had been in the chapel four years ago for the funeral of another famed admiral, Arleigh Burke. Burke, said Clinton, was remembered as the spirit of the Navy.

"They will certainly remember that Bud Zumwalt was its conscience," Clinton said.

One word--"Reformer"--was printed underneath Zumwalt's name and rank on the funeral program. It served as a reminder that despite the honors being paid him yesterday, many in the Navy establishment three decades ago reviled Zumwalt and his fight to promote equality for minorities and women in the service.

There also were reminders of a family tragedy that followed from the service of the admiral and his son Elmo R. Zumwalt III in Vietnam. The admiral's grandson, Elmo Russell Zumwalt IV, born with severe learning disabilities attributed to his father's exposure to Agent Orange, accompanied his sister Maya Zumwalt to the altar for a Scripture reading.

After the service, with a Navy band leading the way and a gun firing in salute, the procession marched through the academy grounds and crossed College Creek on the way to the Naval Academy cemetery.

Accompanying the casket on the journey across the water, three men walked with their own memories of the admiral.

He worried Emmett Tidd, the captain who was chief of staff to Zumwalt when he served as a vice admiral commanding U.S. naval forces in Vietnam.

Zumwalt would read the overnight combat reports as he was driven from his Saigon headquarters at 5 a.m. to a waiting helicopter.

Tidd recalled that the admiral would ask, " 'Where was it the worst?' He wanted to be there to see what he could do, what he could learn."

Many officers, Tidd included, fretted about the admiral's visits.

"They were in very remote locations frequently, and there was always the potential for harm out there. We had no front line. The enemy could be anywhere. Occasionally, he would spend the night out in the field, which would scare the hell out of me," said Tidd, who retired as a vice admiral and now lives in Alexandria.

After arriving in Vietnam in 1968, Zumwalt began using swift boats to aggressively challenge enemy use of the waterways as supply routes. One of the things Zumwalt learned from his forays into the field was the potential a defoliant named Agent Orange might have for saving the lives of sailors.

"He saw the success that the Army was having using it to open up areas that were covered up," Tidd said. "That's the way it originated. He saw an immediate application in rivers and canals."

Casualties among the crews of the swift boats soon dropped to one-sixth what they had been.

Tidd recalled the admiral's reaction when he received a letter from his son, Elmo Zumwalt III, saying he had volunteered for duty in Vietnam commanding a swift boat. Adm. Zumwalt did not intercede, and soon the young lieutenant was taking a swift boat on dangerous patrols through the Ca Mau peninsula.

That's not to say the admiral did not worry about his son. "Every day he did," Tidd said.

In the fall of 1972, racial incidents aboard the carriers Constellation and Kitty Hawk brought criticism of Zumwalt from those who said that as chief of naval operations he had allowed a loosening of discipline.

"Congress was trying to fire him. Nixon was trying to fire him," recalled Bill Thompson, who served in those years as Zumwalt's spokesman.

Zumwalt had been brought back from Vietnam in 1970 to become the youngest chief of naval operations in the nation's history, over the protests of the older Navy establishment.

"The previous CNOs were all southern, and I knew personally they didn't give a damn about minorities, particularly blacks," Thompson said. "Bud changed that."

Jim Zumwalt, like his older brother, Elmo III, never had any doubt that he would grow up to serve in the military.

"My father never sat us down and said you have to serve your country," he said. "We knew it from osmosis."

Jim Zumwalt fought as a Marine in Vietnam. Both brothers made it home. When Elmo III was found in 1983 to have cancer, an illness subsequently linked to his exposure to Agent Orange during the war, Jim Zumwalt was embittered.

"In my case, I started developing quite a bit of animosity toward the war and toward the Vietnamese," said Zumwalt, now in his early fifties and a lawyer in Reston.

"My father turned it into something positive."

The retired admiral studied Agent Orange and its links to cancer, playing an important role in persuading the Veterans Administration to help its victims and insisting that the chemical and cancers were linked.

"My father, with no medical training, showed how the studies were flawed," Jim Zumwalt said. "To his dying day, he felt the decision to use Agent Orange in Vietnam was the right one. The losses we were taking were so high."

After Elmo III died in 1988 at age 42, the retired admiral continued to work for victims, helping to set up a marrow donation program. In the midst of the family's tragedy, Jim Zumwalt said his father had taught him another lesson.

"He was my life's hero," Jim Zumwalt said.

CAPTION: Mouza Zumwalt, escorted by daughter Ann F. Coppola and President Clinton, follows her husband's casket from the memorial service at the Naval Academy chapel.

CAPTION: Sailors march to Zumwalt's grave. As chief of naval operations, Zumwalt pushed the Navy to provide equal treatment for minorities and women in the ranks.

CAPTION: Sailors sound a salute to Adm. Elmo R. Zumwalt Jr. as his funeral procession passes on the way to the Naval Academy cemetery.