In the early days of World War II, a baby-faced West Point graduate with a rifle in one hand and a tommy gun in the other made a one-man attack in the Philippines against the invading Japanese that altered the course of the war.

Jumping from foxhole to foxhole in the jungle, he downed enemies with grenades, gunfire and eventually his bayonet before he was killed. The attack repelled an advance that delayed the Japanese for months, and within weeks the soldier, 23-year-old First Lt. Alexander Nininger, was awarded the first Medal of Honor of the war.

In the decades since, he has been venerated with a statue, an annual award at West Point and even a Malcolm Gladwell treatise on human potential. But his body has not been found. The Army officially lists him as “nonrecoverable.”

His family disagrees. It says the lieutenant’s bones rest in grave J-7-20 at the American Cemetery in Manila. For 70 years, the family has been pressing the military to identify the remains and bring the fallen lieutenant home.

Now, the family and six other families of soldiers buried as “unknowns” in Manila are suing the Department of Defense to compel it to identify the bodies. In a complaint filed in federal court Thursday, they argue that by not using readily available DNA testing to identify the remains, the department is flouting its legal duty to track down “missing persons from past conflicts or their remains after hostilities have ceased.”

Interactive Feature | Searching for Their Unknown Soldiers Several families of soldiers missing in action in Manila are suing the Department of Defense to compel them to identify the bodies.

Among the missing dead are a defiant general killed by a firing squad after he refused to aid the Japanese, a colonel cut down by machine guns during the Americans’ last stand on the Bataan Peninsula and a private who died months later in a Japanese prison camp of dysentery and bayonet wounds.

In the confusion of warfare, all were buried in graves labeled “unknown,” but the families say that in the years since, they have compiled enough evidence to once again give names to the nameless.

“It seems like the least we could do,” John Patterson, 80, Lieutenant Nininger’s nephew, said in an interview in his study in North Kingstown, R.I., where bookshelves sagged with research compiled in an effort to bring his uncle’s body home. “He was a real hero who sacrificed himself.”

The target of the suit is the Defense P.O.W./M.I.A. Accounting Agency, an arm of the Pentagon with a $115 million annual budget that is tasked with accounting for the roughly 45,000 recoverable lost service members dating back to World War II. For years, the agency and a group of agencies that preceded it have been plagued by reports of waste and dysfunction.

Despite its hefty budget, the recovery effort has averaged fewer than 90 bodies annually in the past five years. Congress, frustrated by the low numbers, mandated that the agency increase the number to at least 200 per year by 2015, but it has yet to meet that total.

The agency said connecting remains with lost fighters was a meticulous process that often took years. It has tried to streamline the effort, and identified a record 164 remains in 2016, but staff members warned in recent interviews that extracting usable DNA from 70-year-old remains damaged by the chaos of battle would continue to be a plodding endeavor.

“We completely understand there is frustration and pain of families,” said John Byrd, the director of the agency’s lab. “We are going to do the best we can to ramp up the most robust capability while trying to do the work properly.”

But many families have run out of patience. Lieutenant Nininger’s family has been rebuffed by the agency for decades, even though the family claims it can literally draw a map to his grave site and has provided DNA to make a match.

“We’re not talking Sherlock Holmes here. We’re not even talking ‘Murder, She Wrote.’ Many of these cases are imminently solvable,” said Rick Stone, a former police chief and forensics professor who was deputy of the agency’s World War II branch from 2011 to 2012. “But the system is so dysfunctional that they resist all efforts.”

During his year at the agency, he said, he found 179 cases where the identity of a body could be narrowed to a few names and easily identified through DNA. The agency acted on none, and he soon quit.

Lieutenant Nininger was an unlikely war hero. At West Point, the soft-spoken cadet from Florida gravitated to theater and liked listening to Tchaikovsky. But when the Japanese stormed the Philippines shortly after the attack on Pearl Harbor, it was as if a switch flipped, his nephew said.

Lieutenant Nininger volunteered to go to a spot on the front lines that had splintered under the pounding of a larger Japanese force. With a satchel of grenades and a gun in each hand, he crept through a grove of mango trees and surprised the enemy at close range.

He was wounded three times but kept going. After he ran out of ammunition, witnesses said, he killed three more men with his bayonet, then collapsed. He was wrapped in tent canvas and buried in a hasty grave in a churchyard. A few months later, Americans on the island surrendered.

Ever since, his resting place has been in dispute. After the war, the Army assigned unidentified bones found in a churchyard grave the number X-4685 and reburied them, along with thousands of others, in the American Cemetery in Manila.

Veterans from the lieutenant’s battalion told the family that the grave held the fallen hero, and Army grave technicians sorting remains at the time concurred. The workers concluded twice that X-4685 was Lieutenant Nininger, citing matching dental records and other details. But the central office overruled the identification, saying the bones appeared to be a few inches too short.

In 1951, the agency closed the case, labeling him “nonrecoverable,” and sent a letter to his parents saying, “It is regretted that there is no grave at which to pay homage.”

“I don’t think my mother ever got over it,” said Mr. Patterson, a former Rhode Island state senator. In the decades since, his beard has grown white as he has tried to bring his uncle home.

In the 1960s, at the urging of his mother, Mr. Patterson wrote letters to the Department of Defense asking about the grave, but got only stock responses that the body was lost.

In the 1970s, he began rooting through historical accounts of the battle for clues.

In the 1980s, he tracked down witnesses the Army had never spoken to: a scout who had conveyed the body to the churchyard, an intelligence officer who drew a map showing an ancient mango tree 50 paces southwest of the church, next to the spot where the lieutenant was buried.

“It became my avocation,” Mr. Patterson said. “Some in my family would say my obsession”

In the 1990s, he made a pilgrimage to the churchyard, then tracked the remains to the Manila American Cemetery, where a white marble cross at grave J-7-20 bears the words “Here rests in honored glory a comrade in arms known only to God.”

He asked the Department of Defense again to exhume the grave in 1993. The request was denied. He asked in 2015. It was denied again. He requested instructions on how to appeal the denial. He never got a response.

Agency anthropologists warn that the messy confusion of combat is often preserved in World War II’s many graves. Single coffins can hold multiple skeletons. Bones are often broken and commingled. And burned and degraded remains can make extracting DNA unlikely.

“It’s not as straightforward as pointing to a grave,” said Greg Gardner, chief of the Army’s Past Conflicts Repatriations Branch, “We still have a lot of unknowns.” He added that he was not sure who is in grave J-7-20.

Mr. Patterson hopes a lawsuit will force the agency to find out. And in the process, he hopes Lieutenant Nininger’s case will compel the government to identify hundreds of other missing soldiers.

“Once again maybe he can lead,” Mr. Patterson said. “This time from the grave.”