Mr. Ito’s resignation came less than a day after an article in The New Yorker described the measures that he and other media lab officials took to conceal its relationship with Mr. Epstein. The internal emails, which a former media lab employee shared with The New York Times, described the handling of donations that Mr. Epstein made and apparently solicited from the rich and powerful over the years, including a $2 million gift from the Microsoft co-founder Bill Gates.
In an email in October 2014 — six years after Mr. Epstein had pleaded guilty to a sex charge involving a minor in Florida — Mr. Ito wrote that the gift from Mr. Gates had been “directed by Jeffrey Epstein.” A development official at the media lab, Peter Cohen, wrote in a subsequent email, “For gift recording purposes, we will not be mentioning Jeffrey’s name as the impetus for this gift.”
In a statement, a spokesman for Mr. Gates said Mr. Epstein had been introduced to Mr. Gates as a person interested in helping increase philanthropy. “Although Epstein pursued Bill Gates aggressively, any account of a business partnership or personal relationship between the two is simply not true,” the statement said. “And any claim that Epstein directed any programmatic or personal grant making for Bill Gates is completely false.”
Mr. Gates — one of the world’s richest men and perhaps its most generous philanthropist — is one of many powerful people to face scrutiny for their connections to Mr. Epstein. President Trump and former President Bill Clinton have been forced to explain their associations with him. So have Britain’s Prince Andrew, high-profile scientists and business executives including Leslie Wexner, the chief executive of L Brands, and Leon Black, the founder of Apollo Global Management, one of the world’s biggest private equity firms. R. Alexander Acosta, who as a federal prosecutor was involved in the plea agreement with Mr. Epstein in 2008, stepped down as labor secretary after that deal was heavily criticized.
Mr. Ito’s resignation from M.I.T. was followed in quick succession by announcements from other organizations.
The MacArthur Foundation said reports about his actions, if true, were not in keeping with its values. “Most importantly, our hearts go out to the girls and women who survived the abuse of Jeffrey Epstein,” the foundation said in a statement.
A.G. Sulzberger, the publisher of The Times, and the company’s president, Mark Thompson, wrote an email to staff members that Mr. Ito had stepped down, effective immediately. “Our newsroom will continue its aggressive reporting on Mr. Epstein, investigating both the individuals and the broader systems of power that enabled him for so many years,” they said.
Signe Swenson, who served as a development associate and alumni relations coordinator at the M.I.T. Media Lab from 2014 to 2016, shared the internal emails concerning Mr. Epstein with The Times. She said she had told supervisors several times of her “disgust” at Mr. Epstein’s involvement.
“That was never listened to,” Ms. Swenson, who worked under Mr. Cohen, said in an interview on Saturday. Ms. Swenson shared the correspondence after consulting with the organization Whistleblower Aid.
She said she learned of Mr. Epstein’s connection with the media lab when she interviewed for a position in March 2014, and told Mr. Cohen that M.I.T. listed Mr. Epstein as “disqualified” as a donor. She said Mr. Cohen replied that Mr. Ito had a relationship with the wealthy financier. In one 2014 email that Ms. Swenson shared, Mr. Ito wrote about a $100,000 donation from Mr. Epstein, asking the development staff members to “make sure this gets accounted for as anonymous.”
Mr. Ito took over the Media Lab in 2011 following a rapid ascent in the tech world that made him an unorthodox choice to lead an academic program, but not the freewheeling media lab. He was a two-time college dropout who had run a nightclub, then ran a string of internet companies and invested early in Twitter, Kickstarter and Flickr.
He was also a master networker — one who visited the Obama White House to discuss artificial intelligence and became friends with the respected Harvard lawyer Lawrence Lessig after criticizing Mr. Lessig’s book when he gave a talk in Japan. Mr. Lessig later put Mr. Ito on the board of Creative Commons, a nonprofit advocate for public intellectual property rights.
Mr. Ito’s ability to connect with both students and wealthy donors had helped him raise at least $50 million for the Media Lab, a sort of academic skunkworks. It has contributed to the development of technology related to touchscreens and GPS, is home to a program dedicated to democratizing access to outer space and hands out $250,000 awards to those “challenging the norms, rules or laws that sustain society’s injustices.”
Mr. Ito faced significant criticism from inside the Media Lab. Two scholars said they would leave at the end of the academic year, with one saying he had urged Mr. Ito not to associate with Mr. Epstein. While Mr. Ito did enjoy the support of many within the lab, there were calls for his resignation.
“We have worked literally for years to try to make STEM fields safe and welcoming, attractive fields for women and girls in the face of crushing sexism and gender bias,” said Kim Holleman, an artist who was a visiting scholar and a research affiliate at the media lab from 2013 through 2017. “It’s humiliating to know that men in these institutions, in 2019, still think so little of women’s dignity and safety.”
At a meeting on Wednesday night with media lab personnel, Mr. Ito said he had “screwed up” by accepting the money, but that he had done so after a review by the university and consultation with his advisers.
On Saturday, the university’s president, L. Rafael Reif, said he had asked M.I.T.’s general counsel to hire an outside law firm to conduct “an immediate, thorough and independent investigation.”
“We are actively assessing how best to improve our policies, processes and procedures to fully reflect M.I.T.’s values and prevent such mistakes in the future,” he wrote in an email to the university community. “Our internal review process continues, and what we learn from it will inform the path ahead.”
The emails provided by Ms. Swenson outlined the informal role that Mr. Epstein played at the media lab. In the correspondence about the donation from Mr. Gates, Mr. Cohen wrote that Mr. Ito “did not talk with Bill Gates” and that the program “did not solicit this money.” In another, from May 2014, Mr. Cohen and Mr. Ito discussed Mr. Epstein helping connect the media lab to Mr. Black, the Apollo Global Management founder, who Mr. Epstein had advised on issues including philanthropy.
Mr. Cohen wrote that Mr. Black wanted to make a large donation “in honor of a friend, who wishes to remain anonymous,” and later asked Mr. Ito to find out from Mr. Epstein whether Mr. Black himself wanted to remain anonymous. One email indicated that Mr. Black had given the media lab a gift of $4 million by wire transfer.
Mr. Cohen also asked Mr. Ito whether Mr. Black would like a thank-you note from M.I.T.’s president. Mr. Black’s preference would be something “you or Jeffrey knows best,” he wrote.
A spokeswoman for Mr. Black did not comment on Saturday. Mr. Black has sought to distance himself from Mr. Epstein, describing his interactions with him as limited to tax strategy, estate planning and philanthropic advice. He has also said Apollo had never done business with Mr. Epstein.
Mr. Cohen, now the director of development for computer and data science initiatives at Brown University, did not respond to messages seeking comment on Saturday.