In her late September inauguration, Claudine Gay looked out at a packed audience and spoke of her pride in making history as the first Black president of Harvard in its 387 years.

“I stand before you on this stage, in this distinguished company and magnificent theater,” she intoned before continuing, “with the weight and honor of being a ‘first’ — able to say, ‘I am Claudine Gay, the president of Harvard University.’”

After her resignation on Tuesday, she talked about race very differently. “Those who had relentlessly campaigned to oust me since the fall often trafficked in lies and ad hominem insults, not reasoned argument,” she wrote in a Wednesday opinion piece in The New York Times. “They recycled tired racial stereotypes about Black talent and temperament. They pushed a false narrative of indifference and incompetence.”

The painful and startling story of Dr. Gay’s brief presidency is igniting discussions of plagiarism, fairness, antisemitism and leadership. But also at its core is the unavoidable American question of race, and what role it plays in who gets ahead and how they are judged.

Her appointment came as the country was debating how to balance racial diversity and academic merit, frame history lessons about slavery and racism, and address the needs of Black and poor students.

Just as Dr. Gay took over at Harvard in July, the Supreme Court banned race-conscious admissions at colleges and universities, a decision that sprung from a lawsuit aimed at Harvard.

State legislators have enacted laws limiting what can be taught about America’s racial history. Conservative politicians and activists have targeted university programs seeking to boost diversity, equity and inclusion, and roughly 30 states are considering legislation to curb such efforts.

With its $50 billion endowment, Harvard might seem like it could soar over such battles. But the school’s elite status and the symbolism that it carries have dragged Harvard, and its leadership, straight into the fray.

“I am saddened by the inability of a great university to defend itself against an alarmingly effective campaign of misinformation and intimidation,” Randall Kennedy, a prominent Harvard legal scholar, wrote in a text message.

When Dr. Gay was installed as president of Harvard, supporters hailed her as the fresh, bold face of change. The school would now be led by the Black daughter of Haitian immigrants, a radical departure for a university with a past marred by racism and a lineage of presidents who were exclusively white and, in all but one instance, male.

Dr. Gay “embodies the path that Harvard is on,” said Natalie Sadlak, a medical student who spoke at the September inauguration. The new president, Ms. Sadlak said, represented a blending of the university’s “future and its past, a mixture of the legacy of the university and the promise of new perspectives.”

But from her earliest days in her new role, Dr. Gay operated under heightened scrutiny, with critics eager to question her qualifications and embrace of diversity and equity programs.

Opponents of efforts to diversify American campuses reacted to her promotion scornfully. Yes, since 2015, she had been a powerful administrator at the school, most recently the dean of the sprawling Faculty of Arts and Sciences. But critics argued that her scholarship was relatively thin compared with former Harvard presidents.

Adding to an already toxic brew: the clash over campus culture and politics. And Dr. Gay made enemies quickly.

In 2019, as dean, she issued a two-year, unpaid suspension to Roland Fryer, a Black economist and recipient of a MacArthur “genius grant” who was accused of sexual harassment and creating an unwelcome environment in his education research lab.

Though he has returned to the university, his research lab has been disbanded. Critics say Dr. Gay targeted Dr. Fryer because he published work that went against liberal orthodoxy.

She also had a run in with Ronald Sullivan, a Black Harvard law professor and criminal defense lawyer. Students had protested his decision to represent the film producer Harvey Weinstein against rape and related charges. This role, they claimed, disqualified him from serving as dean of Winthrop House, an undergraduate residency hall.

Harvard decided not to renew his appointment and Dr. Gay criticized him, sparking outrage from the law school faculty and leading conservatives who said that the university had caved to overly sensitive undergraduates.

Dr. Gay might still be president, however, if not for her clumsy handling of the campus conflict over the Hamas attacks in Israel on Oct. 7 and the war in Gaza. Asked at a congressional committee hearing in December whether calling for the genocide of Jews would be harassment under Harvard’s code of conduct, Dr. Gay equivocated and lapsed into legalese.

“It can be,” she said, “depending on the context.”

Her missteps galvanized her opponents.

Bill Ackman, a Harvard graduate and financier, claimed on social media that in their search for president, Harvard’s board members had considered only candidates like Dr. Gay who fit neatly into the university’s goals to become more diverse.

He claimed this filtering was likely common at elite universities. Such a practice, he said, was “not good for those awarded the office of president who find themselves in a role that they would likely not have obtained were it not for a fat finger on the scale.”

A few days after the congressional hearing, accusations that Dr. Gay had plagiarized words and phrases in her scholarship handed her opponents further ammunition.

“She is hardly a ‘scholar’s scholar’, as the university magazine tried to portray her,” wrote Christopher Rufo, the conservative activist who helped make critical race theory a conservative rallying cry. He went on to attack her as a “dutiful racialist, skilled at the manipulation of guilt, shame and obligation in service of institutional power.”

Dr. Gay tried to weather the plagiarism charges. But what began as a drumbeat became a chorus of clamoring doubt that was impossible to ignore, especially as more lapses in her work surfaced.

“I see Gay as getting her post at Harvard because she was a diversity, equity and inclusion candidate, not on the basis of strong academic qualifications,” read a Dec. 21 statement by Vernon Smith, a Harvard graduate and winner of the 2002 Nobel Prize in economics. “There are plenty of accomplished blacks who need no such ‘help.’”

“She is a discredit to Harvard,” he added.

What becomes of Dr. Gay now? She says she plans to return to her role as a Harvard professor.

Even then, she may well carry a weight familiar to many African Americans. She is now a symbol — scorned by some, hailed by others, caught in a whipsawing argument over merit, rights and race that seems to have no end.

Sarah Mervosh and Dana Goldstein contributed reporting.

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