While top Harvard officials typically rubber-stamp departmental admissions decisions, in this case the university’s leadership — including the president, provost, and deans of the graduate school — reversed one, according to the emails and interviews, out of concern that her background would cause a backlash among rejected applicants, conservative news outlets or parents of students.

The admissions dean of Harvard’s Graduate School of Arts and Sciences declined to be interviewed, and a university spokeswoman did not respond to a set of eight questions about the case, saying that “as a policy, we do not comment on individual applicants.”

Instead, the spokeswoman offered a general statement saying the graduate school “is committed to recruiting and enrolling students from all backgrounds” and “strives to create an inclusive and supportive environment where all students can thrive.”

Harvard has, indeed, made room for a wider range of voices on its campus in recent years, including the formerly incarcerated. Drew Faust, a historian who is departing as Harvard’s president in June after a decade, has expanded global outreach and financial aid, and hired a host of minority faculty who have broadened perspectives about prison reform and black culture.

In that mode of outreach, staff members of both Harvard’s history and American studies departments took it upon themselves to type Ms. Jones’s application into Harvard’s online system since she could not.

But after the history department accepted her and the American studies program listed her as a top alternate, two American studies professors flagged Ms. Jones’s file for the admissions dean of the Graduate School of Arts and Sciences. In a memo to university administrators, these professors said the admissions dean had told them Ms. Jones’s selection would be reviewed by the president and provost, and questioned whether she had minimized her crime “to the point of misrepresentation.”

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“We didn’t have some preconceived idea about crucifying Michelle,” said John Stauffer, one of the two American studies professors. “But frankly, we knew that anyone could just punch her crime into Google, and Fox News would probably say that P.C. liberal Harvard gave 200 grand of funding to a child murderer, who also happened to be a minority. I mean, c’mon.”

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Ms. Jones got pregnant at 14 after what she called non-consensual sex with a high-school senior. Her mother responded by beating her in the stomach with a board, according to the prosecutor who later handled her case, and she was placed in a series of group homes and foster families.

In a personal statement accompanying her Harvard application, Ms. Jones said she had a psychological breakdown after years of abandonment and domestic violence, and inflicted similar treatment on her own son, Brandon Sims.

The boy died in 1992 in circumstances that remain unclear; the body was never found.

Two years later, during a stay at a mental-health crisis center, Ms. Jones admitted that she had buried him without notifying the police or Brandon’s father and his family. At her trial, a former friend testified that Ms. Jones confessed to having beaten the boy and then leaving him alone for days in their apartment, eventually returning to find him dead in his bedroom.

Ms. Jones was sentenced to 50 years in prison, but was released after 20 based on her good behavior and educational attainment.

In her statement to Harvard, Ms. Jones wrote of Brandon: “I have made a commitment to myself and him that with the time I have left, I will live a redeemed life, one of service and value to others.”

Brandon’s father and grandmother could not be reached for comment.

Where Were the Ladies?

Incarcerated in 1996, Ms. Jones worked for five years in the law library at Indiana Women’s Prison, and got certified as a paralegal. She received a bachelor’s degree from Ball State University in 2004, and audited graduate-level classes at Indiana University.

Her blossoming as a historian began in 2012, when Kelsey Kauffman, a former professor who volunteered at the prison, encouraged inmates to research the origins of their involuntary home, which opened in 1873 as the first adult female correctional facility in the United States. Soon, Ms. Jones was placing library requests for reference books and, when they arrived months later, scouring the footnotes for what to order next.

After meticulously logging demographic data from century-old registries from the Indiana Women’s Prison, Ms. Jones made a discovery: There were no prostitutes on the rolls. “Where,” she asked, “were all the ladies?” meaning so-called ladies of the night.

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With the help of a state librarian, she and another inmate realized that a Catholic laundry house that opened around that time in Indianapolis was actually a reformatory for “fallen women” — those convicted of sex offenses. Then they found more than 30 similar institutions around the country, akin to the Magdalene Laundries recently unearthed in Ireland.

Under Ms. Kauffman’s tutelage, they wrote up their findings, published them in an Indiana academic journal, and won the state historical society award. Ms. Jones also presented the paper remotely at multiple academic conferences, and, at others, shared different work about the abuse of early inmates at Indiana Women’s Prison by its Quaker founders.

Ms. Jones was supposed to be released in October, but received a two-month reduction of her sentence so she could start a Ph.D. program on time this fall. She applied to eight, with Harvard her first choice because of historians there whose work on incarceration she admired.

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While those historians embraced her application, others at Harvard questioned not only whether Ms. Jones had disclosed enough information about her past, but whether she could handle its pressure-cooker atmosphere.

“One of our considerations,” Professor Stauffer said in an interview, “was if this candidate is admitted to Harvard, where everyone is an elite among elites, that adjustment could be too much.”

Alison Frank Johnson, director of graduate studies for the history department, dismissed that argument as paternalistic.

“Michelle was sentenced in a courtroom to serve X years, but we decided — unilaterally — that it should be X years plus no Harvard,” she said. “Is it that she did not show the appropriate degree of horror in herself, by applying?

“We’re not her priests,” Professor Johnson added, using an expletive.

A Sentence Completed

Over the past decade, some universities, corporations, and state and local governments have begun to break down barriers that block formerly incarcerated people from education and employment. A “ban the box” campaign by civil-rights groups led scores of institutions, including Harvard’s graduate schools, to remove a question about criminal records from their initial applications.

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But most of these efforts focus on giving a fresh start to nonviolent offenders, especially those caught up by tough sentencing laws for drug crimes.

“It’s like we only have enough imagination — and courage — to envision second chances for the people who shouldn’t have been in prison in the first place,” Professor Johnson said.

Ms. Jones’s many supporters include Heather Ann Thompson, who won the Pulitzer Prize in history this spring, and submitted a recommendation letter on her behalf. There is also Diane Marger Moore, the prosecutor who argued that Ms. Jones receive the maximum sentence two decades ago and is now writing a book about the case.

“Look, as a mother, I thought it was just an awful crime,” said Ms. Marger Moore, now a lawyer at a large firm in Los Angeles. “But what Harvard did is highly inappropriate: I’m the prosecutor, not them. Michelle Jones served her time, and she served a long time, exactly what she deserved. A sentence is a sentence.”

Her backers saw her background as an asset, given the growing academic interest in incarceration.

“It was a chance for us to do something that we’ve been saying we’re trying to do at Harvard, which is to set up conversations between academics and eyewitnesses,” said Walter Johnson, director of an American history study center at the university.

But the American studies professors said in their memo to administrators that “honest and full narration is an essential part of our enterprise,” and questioned whether Ms. Jones had met that standard in framing her past. In the personal statement, which was not required, she did not detail her involvement in the crime, but wrote that as a teenager she left Brandon at home alone, that he died, and that she has grieved for him deeply and daily since.

Professor Stauffer emphasized in interviews that he and his departmental colleague, Dan Carpenter, were simply trying to ensure that Harvard did its due diligence about the candidacy.

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“We do not want to stand in the way of, advance a case against, or in any way hijack the career of Michelle Jones, who has served her time, who has clearly done amazing things while incarcerated, who shows passion for her craft, and whose full story the two of us can never really know,” they wrote in the memo.

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“If officials who take a careful look at the case decide that Harvard should move forward, then we think that the university should do everything in its power and ability to welcome Ms. Jones here and support her, and we are indeed happy to play a part in that effort,” they continued. “We have stated our concerns as questions, and we hope they are treated as nothing more nor less than questions, not as an implicit or explicit judgment against a person and her candidacy.”

Ms. Jones, in an interview, said that if anyone at Harvard wanted her to elaborate on the criminal case or her preparedness for the Ph.D. program, they should have asked. “I just didn’t want my crime to be the lens through which everything I’d done, and hoped for, was seen,” she said.

“I knew that I had come from this very dark place — I was abhorrent to society,” she continued. “But for 20 years, I’ve tried to do right, because I was still interested in the world, and because I didn’t believe my past made me somehow cosmically un-educatable forever.”

The Toughest School

Yale University also rejected Ms. Jones, though it is unclear what role her crime may have played in its decision; officials would not discuss her application.

But she was courted by the University of California, Berkeley; the University of Michigan; the University of Kansas; and N.Y.U., which assigned graduate students to send Ms. Jones welcoming notes on JPay, a prison email app.

She arrived in Manhattan during the back-to-school season of fresh starts, having never used a smartphone. She wore prison-issue glasses and carried boxes full of jailhouse research notes.

If her new parole officer allows it, Ms. Jones hopes to teach in N.Y.U.’s prison education program, as a way to remember where she has been. She also hopes to take the train to Cambridge, Mass., every other week to sit in on a Harvard seminar on the history of crime and punishment in America.

“We’re having her come up here for that partly out of a sense of pique,” Mr. Johnson said.

At N.Y.U., Nikhil Singh, faculty director of the prison-education program, acknowledged that “Michelle will have a lot to prove.”

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“Our hope is that she is actually far, far more resourceful and driven than most college students,” he added, “who take for granted they are supposed to be here.”

On the Friday before classes started, in a lounge on the N.Y.U. campus, Ms. Jones said any presumption that she is not ready for a Ph.D. underestimates her own moxie and “sells prison short.”

“People don’t survive 20 years of incarceration with any kind of grace unless they have the discipline to do their reading and writing in the chaos of that place,” Ms. Jones said. “Forget Harvard. I’ve already graduated from the toughest school there is.”