More than 50 years after his sister was killed, Darryl Malecki watched on Thursday as her body was lowered into her grave, for a second time, at a cemetery in Baltimore.

No one has ever been charged with the killing of Joyce Malecki, who disappeared in November 1969, when she was 20, and was found dead days later on the Fort Meade military base south of Baltimore. But the exhumation of her remains for DNA samples has raised her family’s hopes that the case will finally be solved.

“It is a steppingstone,” Mr. Malecki, 71, said in an interview after his sister’s body was returned to her grave. “They removed from her whatever they needed.”

On Thursday, the F.B.I. confirmed in a statement that it had exhumed Ms. Malecki’s body at Loudon Park Cemetery in southwest Baltimore as part of an investigation into her killing. It gave no further details, but the announcement revived questions about the case, which was featured in a 2017 Netflix documentary series about the death of a nun and allegations of sexual abuse against a local priest.

Two days after Ms. Malecki was reported missing, her body was found in a pond at Fort Meade, a sprawling military base about 18 miles south of Baltimore. She was on her way to meet her boyfriend, a soldier posted at the base, when she disappeared, her brother said. An autopsy determined that she had been strangled.

The Netflix series “The Keepers” examined Ms. Malecki’s death in connection with the killing of the nun, Sister Catherine Ann Cesnik, a 26-year-old English teacher at Archbishop Keough High School in Baltimore. The women went missing within days of each other, and their bodies were found just a few miles apart. People familiar with the case said in the series that Sister Cathy was about to reveal allegations of sexual abuse by the Rev. A. Joseph Maskell, a guidance counselor at the school, when she was killed.

Days before the documentary was released, Archbishop William E. Lori of Baltimore said in a statement that the first suggestion that Father Maskell might have been involved in Sister Cathy’s death was made to the Baltimore Archdiocese in 1994. But Archbishop Lori said that there was no record of Sister Cathy contacting the Archdiocese about Father Maskell and that no criminal charges were filed in connection with her death.

In 1992, Jean Wehner, a former student of Sister Cathy’s, accused Father Maskell of sexually assaulting her when she was in high school. She said that she had confided in Sister Cathy, and that Father Maskell took her to see the nun’s body as a warning against speaking out.

“The Keepers” focused mainly on Sister Cathy’s murder, but it revived accusations of a broader cover-up by the Archdiocese that some of her former students, as well as some who have accused Father Maskell of abuse, say has clouded the investigation into Ms. Malecki’s killing.

Father Maskell died in 2001. In 2017, the Baltimore County Police Department announced that a DNA sample taken from his remains did not match crime scene evidence from Sister Cathy’s killing.

In April, the Maryland Attorney General’s Office released a 463-page report that found “staggering” rates of sexual abuse of children by clergy members across the Archdiocese of Baltimore over the course of six decades, as well as cover-ups by members of the church hierarchy.

The Malecki family lived about a block away from St. Clement Catholic Church, where Father Maskell was a parish priest before he was transferred to Archbishop Keough High School.

Advances in DNA technology and genetic genealogy have helped investigators solve more cold cases in the United States, giving the Malecki family new, if cautious, hope that the authorities might find her killer.

“One of our strongest conjectures about all this is they are not exhuming this young lady after 54 years in a random attempt to gain evidence,” said Kurt Wolfgang, the executive director of the Maryland Crime Victims Resource Center, which has been working with the Malecki family. “We think they have a strong theory or they would not be doing this.”

“If the person who did this is still alive, they want to see him prosecuted,” he said.

Mr. Malecki said that the F.B.I. has told his family that its file on the investigation has grown to 4,000 pages. The bureau has provided no specific information about what, or who, it is looking for, he said.

On Thursday, law enforcement officers closed the cemetery as the exhumation was taking place. After it was over, Mr. Malecki, his older brother Pat and two nieces were escorted to a chapel where Ms. Malecki’s coffin was waiting.

“We went into the chapel so we could see the casket and say our goodbyes,” he said.

The coffin was placed into a hearse and taken to the same plot where she was buried 54 years ago. It was lowered into the cement vault, and a backhoe refilled it with earth.

Mr. Malecki said he was the last member of his family to see his sister alive. He was working a late shift at a fast-food chain called Gino’s in Baltimore. It was Nov. 11, 1969, and Ms. Malecki stopped by to swap her Pontiac for their parents’ 1967 Chevrolet Impala, which Mr. Malecki had taken to work. She was on her way to meet her boyfriend and do some shopping.

“I guess she felt more comfortable in a new car,” Mr. Malecki said.

She never came home. Two days later, two hunters found her facedown in a creek, he said.

“My sister was only 20 years old, in her prime,” he said. Reflecting on the life that was still ahead of her, he said, “She was robbed of all that.”