Sage Ross / DPA / LANDOV Aaron Swartz committed suicide on Jan. 11, 2013, shortly before a trial against him.

The Massachusetts Institute of Technology has launched an internal investigation into the school’s involvement in the suicide of 26-year-old computer programmer and Internet activist Aaron Swartz, MIT’s president L. Rafael Reif said on Sunday. Swartz was accused of breaking into MIT’s computer system in order to access academic articles and make them available for free on the Internet.

Before he died last Friday, Swartz, who was a well-known computer programmer — but not an MIT student — faced a 35-year prison sentence on federal data-theft charges for illegally downloading articles from the subscription-based academic research service JSTOR. Swartz had allegedly broken into a secure MIT computer closet on at least one occasion and hooked up a laptop in order to download JSTOR files, before he was arrested in 2011 by Cambridge, Mass., police.

Swartz, who was considered one of the brightest young minds in tech activism, hanged himself on Friday night in his Brooklyn apartment. He had been struggling with depression for many years. Swartz’s partner, Taren Stinebrickner-Kauffman, was the first person to find him, according to the Wall Street Journal. There was no apparent suicide note, officials said.

Swartz’s death cast a pall over the tech world and prompted soul-searching questions among policy experts and university officials — not to mention his grieving family and friends. Swartz’s passing triggered an outpouring of grief from those who knew him well, and the broader technology and Internet community.

(MORE: Aaron Swartz, Tech Prodigy and Internet Activist, Is Dead at 26)

MIT, one of the nation’s most prominent and respected universities, has come under criticism for its handling of the Swartz affair. In July 2011, JSTOR said it would drop any civil claims against Swartz. According to Lawrence Lessig, who runs Harvard University’s Edmond J. Safra Center for Ethics, where Swartz was a fellow in 2011, MIT fell short by not following JSTOR’s lead.

As if that wasn’t enough, hours after MIT issued its statement on Sunday, the university’s website was disabled by unknown cyberassailants. The Tech, an MIT school newspaper, reported: “MIT’s network fell to a denial-of-service attack Sunday evening, allegedly by the Internet activist group called Anonymous, cutting campus users off from Internet access to most websites for nearly three hours.”

“Early on, and to its great credit, JSTOR figured ‘appropriate’ out,” Lessig wrote. “They declined to pursue their own action against Aaron, and they asked the government to drop its. MIT, to its great shame, was not as clear, and so the prosecutor had the excuse he needed to continue his war against the ‘criminal’ who we who loved him knew as Aaron.”

Prior to his death, Swartz faced up to 35 years in prison and a fine of up to $1 million for the alleged JSTOR downloads. He had pleaded not guilty. His trial was set to begin next month. Several prominent observers, including Lessig, called the potential penalty disproportionate to the alleged crime.

In a statement, JSTOR officials sent condolences to Swartz’s family and friends. “The case is one that we ourselves had regretted being drawn into from the outset, since JSTOR’s mission is to foster widespread access to the world’s body of scholarly knowledge,” the nonprofit academic organization said.

For its part, Swartz’s family criticized the way MIT — and the federal government — have handled the case. “Aaron’s death is not simply a personal tragedy,” his family wrote. “It is the product of a criminal-justice system rife with intimidation and prosecutorial overreach. Decisions made by officials in the Massachusetts U.S. Attorney’s office and at MIT contributed to his death.”

Swartz’s lawyer, Elliot Peters, had made overtures to Assistant U.S. Attorney Stephen Heymann aimed at settling the charges, according to the Wall Street Journal. But Heymann insisted that Swartz plead guilty and face jail time, and Heymann wouldn’t budge from that position, according to the paper. Heymann works for Massachusetts U.S. Attorney Carmen Ortiz, who has faced criticism over her handling of the case.

In a statement, MIT president Reif sought to strike a conciliatory note. “I want to express very clearly that I and all of us at MIT are extremely saddened by the death of this promising young man who touched the lives of so many,” he said. “It pains me to think that MIT played any role in a series of events that have ended in tragedy.”

Reif said he’s asked Hal Abelson, a professor of electrical engineering and computer science at MIT, and a founding director of Creative Commons and the Free Software Foundation, to lead the investigation into MIT’s actions leading up to Swartz’s suicide. “Now is a time for everyone involved to reflect on their actions, and that includes all of us at MIT,” Reif wrote.

Here’s the letter that MIT president Reif wrote to his community on Sunday.