Mr. Protess, who taught at the Medill journalism school at Northwestern University, was the founder and driving force behind the Medill Innocence Project, which was instrumental in exonerating at least 12 wrongly convicted defendants and freeing them from prison, including five who were on death row in Illinois, and in prompting then-governor George Ryan to clear the rest of death row in 2003.

But during an investigation into a questionable conviction, the Cook County state’s attorney turned her attention instead on Mr. Protess and his students. Since then, questions have been raised about deceptive tactics used by the Medill students, about allegations that Mr. Protess cooperated with the defense lawyers (which would negate a journalist’s legal privilege to resist subpoenas) and, most damning, whether he altered an e-mail to cover up that cooperation.

Medill, which enjoys an international reputation, in significant part because of his work, removed him from teaching in April, and this week he resigned from Northwestern altogether. It has been a breathtaking reversal for Mr. Protess, who says he believes he is being pilloried for lapses in memory and a desire to defend his students.

“I have spent three decades exposing wrongful conviction only to find myself in the cross hairs of others who are wrongfully accusing me,” he said in an interview.

It is often said that academic politics are so vicious because the stakes are so low, but in the matter of Mr. Protess and the wrongly convicted men he helped to free, the stakes could not have been higher.

“He is in the hall of fame of investigative journalists in the 20th century,” said Mark Feldstein, an associate professor of media and public affairs at George Washington University. “Using cheap student labor, he has targeted a very specific issue, and that work has reopened cases, changed laws and saved lives.”

Dennis Culloton, a lawyer who served as press secretary for Governor Ryan, said that Medill’s work led in part to the decision to essentially shut down Illinois’s death row. “I think it would have been an academic discussion if not for David’s work,” he said.

Behind that public success, however, there were gnawing tensions within Medill. Mr. Protess’s tendency to clash with authority did not end with law enforcement. He came into conflict with at least two deans of the Medill school, including the current one, John Lavine, who started in 2006 after a long career in newspapers.

Mr. Lavine is a polarizing figure at Medill: he is widely credited with stabilizing an institution that was suffering financially but he also led a successful effort to rename the school the Medill School of Journalism, Media, Integrated Marketing Communications, a change he said reflected the school’s broader agenda but one that was widely ridiculed by alumni and journalists.

Mr. Protess said the project initially received support from the dean, but now says that was a charade, “an attempt to seem as if he were fighting for the First Amendment when in fact he was undermining the Innocence Project at every turn.” Mr. Lavine counters that he had no choice but to remove Mr. Protess: “What I saw warranted the decision that I made.”

Mr. Protess (whose son Ben is a reporter for The New York Times) started the Innocence Project at Medill in 1999 after spending much of his career looking into questionable convictions for Chicago Lawyer magazine. Working with the Center on Wrongful Convictions, a sibling project at the Northwestern Law School, Mr. Protess methodically vetted cases, laid out lines of inquiry for his student journalists and guided them through their reporting assignments.

As the list of exonerations grew, the global reputation of Medill — and Mr. Protess — soared and students were drawn to the project to be trained in the real-life crucible of capital cases.

“His class was life-changing,” said Evan S. Benn, a former student of Mr. Protess who is now a reporter at The St. Louis Post-Dispatch.

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