Madison Harris came home to Atlanta as a World War II veteran of the Army that helped free Europe and Asia from fascism. But the city he returned to was still a bastion of segregation, and on the clanking streetcar he boarded in April 1946, the separation of the races remained absolute.

Blacks crowded in back; whites up front. When Harris stepped off, witnesses said, the 21-year-old left by the rear exit, as blacks were required to do, and appeared to be unarmed.

Harris had walked only a few steps before the white conductor opened the front door. “Boy, give me that gun,” the driver yelled.

Harris raised his empty hands in the air, but the conductor fired his .45-caliber revolver anyway, witnesses said. Harris died instantly from a single shot to the left temple.

The conductor, T. H. Purl, told police that Harris had been armed and drunk, so they booked Purl on “disorderly conduct — shooting another” and let him go. The following week, Judge A. W. Callaway dismissed even that minor charge.

The killing drew some local notice, but soon the story of Madison Harris was all but lost. Now, nearly 70 years later, a civil rights team at Northeastern University in Boston has dug it up, a fragment from what seemed a distant time in America’s brutal history of race.

Now, after the fury over the recent deaths of unarmed black men in Missouri and New York, it doesn’t seem so distant at all.

Since 2007, Northeastern law students have documented about 350 racially motivated killings, often by piecing together obscure clues buried in government archives and newspaper clippings.

Aided by Northeastern journalism students, they painstakingly pursue a staggeringly ambitious goal: to identify every racially linked murder in the South between 1930 and 1970.

The trail to Madison Harris was uncovered by Alex Cherup, a third-year law student drawn to the task by Margaret Burnham, a Northeastern University professor who worked for voting rights in Mississippi, became the first black female judge in Massachusetts, and was appointed by Nelson Mandela to help investigate human-rights abuses in South Africa.

But bringing to light forgotten murders of the segregation era, Burnham said, is the most important work of her life.

“It’s my civic responsibility,’’ said Burnham, who with Massachusetts Institute of Technology professor Melissa Nobles cofounded the law school’s Civil Rights and Restorative Justice Project.

Cherup’s investigative odyssey began in May 2013, when he was handed a file with a few scraps of information about the 1946 death of Walter Lee Johnson, a black World War II veteran killed by a white Atlanta streetcar conductor.

In the moments before the shooting, Johnson had stood on a downtown sidewalk and shouted, “Straighten up and fly right!” to a friend passing in an automobile.

The expression came from a popular song by Nat King Cole, but the conductor in a nearby streetcar apparently thought Johnson was taunting him, witnesses said.

The conductor stopped the streetcar and strode up to Johnson. “Repeat those remarks,” he snapped. A scuffle followed, and the conductor shot Johnson.

Johnson died the following morning, leaving a 3-year-old child and a pregnant wife.

Cherup learned that the shooting, at a site now buried by concrete near the Georgia Dome football stadium, was not an isolated spasm of violence. He read of frequent police brutality against black veterans in 1946 and of a lynching that summer in which four blacks, one of them a veteran, were killed 60 miles east of the city.

And he read, almost as an aside in a news article, that a few months before Johnson’s death an Atlanta streetcar conductor had killed another black veteran — Madison Harris. All of Atlanta’s streetcar conductors were white and armed at the time.

Callaway, the judge who had dismissed Harris’ death as “a case of justifiable homicide,” reached the same decision in Johnson’s case. “No jury on Earth would convict him,” Callaway said of W.D. Lee, the motorman who killed Johnson.

Seeking Justice in Modern Atlanta

Part of Burnham’s task is gaining a belated measure of justice, or even acknowledgment, for black people victimized decades ago by a system that valued life according to skin color.

The Northeastern team’s latest success occurred on Dec. 17, when a South Carolina judge exonerated a 14-year-old black youth, George Stinney Jr., who was electrocuted in 1944 in the deaths of two white girls. Burnham’s group fought for the decision.

Now Burnham and her team believe they have found a vehicle for another public reckoning: Atlanta’s streetcars.

The transit line, run by Georgia Power Co. in those troubled postwar years, was discontinued in 1949 as the city grew and changed. But this past week, Atlanta’s streetcars re-emerged in a $99 million project that mixes traffic-thinning pragmatism with nostalgia for a simpler time.

The 2.7-mile streetcar loop will connect downtown with Atlanta’s most important civil rights landmarks, including the Martin Luther King Jr. National Historic Site.

For the Northeastern team, which had not known about the streetcar restoration effort when Cherup began his work, the timing is ideal.

The new line provides an opportunity to remind Atlantans about the city’s past, Burnham believes. One tool could be an informational plaque on the streetcars about past segregation. Another option is to commemorate the deaths of Harris and Johnson with memorial markers.

In Atlanta, at the National Center for Civil and Human Rights, two large photographs starkly capture the consequences of a bygone era that enforced the racial separation of human beings: The faces in the photos — black and white, riding through the streets of the city — are individual studies in dour, sullen discomfort.

Since those days, Atlanta has been transformed: The police force was integrated in 1948. The buses in 1959. The city has had an unbroken string of black mayors since 1974. And black passengers on Atlanta’s new streetcars can sit anywhere they wish.

Atlanta Mayor Kasim Reed said he is open to the idea of officially acknowledging the racial killings of the streetcar days of old — just not as the new streetcar opens for business.

Official recognition “may come in the future when we have a chance to review and digest the information, give some serious thought to it,” Reed said.

Atlanta, Reed said, has historically confronted “issues of race and class” and has produced five Medal of Freedom winners who devoted themselves to the fight for equal rights.

“Our story, overall, is one of forward progress,” he said.

The dean of Georgia’s black state legislators, Rep. Tyrone Brooks of Atlanta, did not know of Harris’ killing, despite decades of work in civil rights.

Nor did M. Alexis Scott, publisher of the Atlanta Daily World, a newspaper founded by her grandfather in 1928 to serve the city’s black population. Or Hamin Dawan, who fought in Vietnam as a combat infantryman and is now commander of Atlanta’s chapter of the National Association for Black Veterans.

And it is unclear whether there is any record or memory of that history at Georgia Power, which operated the old streetcar line. The company did not respond to repeated questions about Northeastern’s findings.

A Legacy That Racism Can’t Restrain

Eight hundred miles to the north in Allentown, Pa., is a modest ranch house where Carlton Shockley sits on a sofa, surrounded by patriotic mementos, among them his paratrooper’s beret from the 82d Airborne Division.

Shockley scans article after article from the Atlanta Daily World of 1946 that Cherup compiled during his detective work. The 52-year-old veteran had heard as a child that Harris, his great-uncle, was shot on a streetcar shortly after World War II. But until this moment, Shockley had never known the details.

He lifts himself from the couch and covers his face with his hands.

“If this isn’t a hate crime, I don’t know what is,” Shockley said. “As a soldier myself, that’s a tough pill to swallow — a soldier coming home to die.”

The shooting devastated Shockley’s father, to whom Harris had been a surrogate big brother.

“My father told me, ‘They shot him. They shot him dead like a dog.’ It broke his heart.”

Shockley wants an official acknowledgment of Harris’ death but said that will not define his great-uncle’s legacy. Instead, Harris is linked in a richer way to what his great-nephew calls “the family business” of U.S. military service.

Some of the family fled north during the Civil War to fight for the Union. Others served in World War I, and three of Harris’ brothers saw duty in Europe during World War II.

Later, Shockley and five siblings entered the military, including a sister who remains an Army master sergeant. A niece is an Army major who served in Afghanistan and Iraq, and Shockley’s two sons have chosen the Air Force.

“We’re going to continue to serve this country, because we’re not going to let the bigoted views of a few prevent us,” Shockley said.