Willie T. "Timmy" Donald, who was convicted of murder in 1992, used to think he had good friends at the Medill School of Journalism. But now associate dean Mary Nesbitt won't even answer his letters. I respect her position but have more sympathy for his.

In late April a letter from Donald came to me from out of the blue. "I've been incarcerated for twenty years for a crime I did not commit," it began. Six years ago he'd asked the famous Medill Innocence Project to help him. "David Protess and his students started investigating my case. I enjoyed working with David and his students because they seemed eager to find the truth. In the early stages of 2009, crucial evidence began to surface, evidence so crucial it had the potential to exonerate me."

But 2009 was the year Protess, founder of the Medill Innocence Project, began his fall from grace. Skeptical of the project's claim that a prisoner named Anthony McKinney was innocent of a 1978 murder, Cook County state's attorney Anita Alvarez subpoenaed the "notes, memoranda, reports and summaries" from the Protess team's investigation. Medill and Northwestern University joined Protess in fighting the subpoena, but in 2010 the alliance collapsed. Medill and the university accused Protess of "knowingly making false and misleading statements" to university attorneys and Medill's dean, and last spring Medill took away his classes. So Protess "retired," declaring that he would launch a new, unaffiliated Chicago Innocence Project, open to students from anywhere.

In the uproar, McKinney's petition for a new trial went nowhere. Donald, following the drama as best he could from a prison cell in Miami, Indiana, felt just as marginalized. "It's been nearly three years since I heard from the MIP," his letter told me. "My family have called and left messages but they never returned their calls. I don't even know the status of my case, because the MIP are refusing to contact me."

Early this year he wrote two letters to Nesbitt. "Since 2009, no progress has been made," said the first. (Donald provided me with copies.) "I would like to move forward so I have decided to go in another direction. . . . I feel comfortable working with Mr. Protess and I would like him to continue to work on my case. I'm giving the Medill Innocence Project permission to hand over my files to Mr. Protess."

Nesbitt did not write back. Donald's second letter made no attempt to hide his desperation. "Since 2009, there has been total silence," he told her. "If I want to move in a different direction, I should have the right to make that decision. Your organization does not have the right to make that decision for me."

Again Nesbitt did not reply to Donald. Then he wrote me.

"They have shoved my case under the rug," he told me, "and have not given me an explanation, as to why they are refusing to let another organization look into my case. I'm writing this particular letter not to bring shame to their organization but to bring to light their disturbing behavior. I want their unfair treatment of me to be known to the public. I hope and pray you will share this information with others. An innocent man is suffering because of their actions."

Nesbitt would not discuss Donald with me on the record.

Donald's troubles date to the night of February 27, 1992, when Gary, Indiana, was hammered by five armed robberies—all believed at first to have been committed by the same gunman, a man described as having an acne-scarred face. One victim, Bernard Jimenez, was accosted in his driveway with his fiancee and young children, and when he resisted he was shot to death.

Gary police happened to have a mug shot of Donald because three years earlier he'd been arrested for auto theft. (The charge was dropped.) Witnesses to the robberies looked at that mug shot among others, and despite Donald's unscarred face two of them picked it out. One was Jimenez's fiancee. The other was Rhonda Williams, who was robbed of $50 by a man who forced his way into her house. The two women later pointed to Donald in a police lineup.

He was convicted and sentenced to 60 years in prison.

The Medill Innocence Project spent three years on the case. Students uncovered a couple of old documents Donald's trial lawyer apparently hadn't seen: a statement from another robbery victim—a policewoman—that it wasn't Donald who robbed her, and a note from the prosecution's pretrial interview with Williams that said she "can't swear in court that the defendant is the person." The students came up with an alternative suspect, and the project paid about $10,000 to run a DNA test of hairs found on Jimenez's jacket in the hope they'd implicate this other man. But they didn't—or Donald either.

And in an on-camera statement taken by Medill investigator Sergio Serritella, Williams repudiated her ID of Donald. She said she'd picked his mug shot out of the pile because his was the only face that resembled the robber's, but she said that later she saw the actual robber outside her home (at a time when Donald was having lunch at work with a supervisor). She also said she and Jimenez's fiancee had looked at the police pictures together—a violation of protocol if it happened. (The fiancee denied it.)

The Medill Innocence Project shared court documents with Times of Northwest Indiana reporter Sarah Tompkins—an Innocence Project alum who'd become aware of Donald's case while working on an unrelated case for Protess. Tompkins wrote several stories on Donald and, like Serritella, made a video of Williams repudiating her identification of Donald.

Serritella's video is the centerpiece of the material that Donald wants Northwestern to release. I asked Protess to comment, and he e-mailed me: "While I was still at Medill, Associate General Counsel Amy Mayber seized our file on the Donald case, including everything from students' reporting memos to police reports and trial transcripts. I asked for the file to be returned so we could continue our reporting, but to no avail.

"This is yet another overreaction by university counsel to State's Attorney Alvarez's subpoena, and it makes no sense since Mr. Donald's case is in Indiana and our relationship with the prosecutors has been cooperative."

The new director of the Medill Innocence Project is Alec Klein, and on his watch the project seems less interested in freeing the innocent than separating itself from the David Protess era.

Mayber had no comment.

I arranged a phone conversation with Donald primarily to ask him why he'd written me. Did Protess put him up to it, to embarrass Medill? No, said Donald, it was at the suggestion of a Denver man named David Lynch. Four years ago, Lynch's daughter Eimear was a Medill senior working on Donald's case. Today she's an editor in New York City but she hasn't put Donald behind her. Moreover, her father now champions Donald's cause. This February her father wrote Nesbitt on Donald's behalf.

"Our whole family has formed a relationship with this gentle, sad man, who had his hopes raised by the Medill students and staff, and cannot understand how he is quite suddenly abandoned without any communication from Northwestern," wrote David Lynch. "I am writing to appeal to you to find a way to release his file so that his attorney and team can continue to work on this case. I understand there are legal concerns, but I think they should be over-ridden in this case by a moral imperative not to let this injustice, which has already gone on much too long, continue."

Nesbitt replied to this e-mail: "I'm afraid the issues are quite substantial, apart from FERPA [Family Educational Rights and Privacy Act] considerations, and there is no getting around them," she explained. "As I explained to Eimear, MIP case files comprise material that was gathered during a journalistic investigation. Medill does its utmost to protect the integrity and legal privilege of that journalistic work. For those important reasons we have adopted a policy that MIP files are not shared outside Medill."

It's a reasonable policy. Northwestern originally fought Alvarez's subpoena on the grounds that the state's attorney was asking for reporters' work product; a principle looks a lot sturdier if it's maintained even when it would be lovely to set it aside. The Times of Northwest Indiana is taking the same position: Donald's attorney, Thomas Vanes, asked for the video of Tompkins's interview with Williams and was told to settle for the portion the Times posted on its website.

There's also the question of how much good the file would do Donald, whose petition for postconviction relief is scheduled to be heard in July. "For the prosecutors, Medill's reputation is such now that nothing they produce will stand on its own," Vanes told me last week. That includes the video of Williams recanting. The prosecutors "are actually willing to listen, and they'd be willing to listen to Rhonda, but not filtered through Medill and not filtered even by me," Vanes said. "They want to talk to the woman themselves—as do I. I'd like to sit her down." The problem is that Williams moved to Florida and now can't be located. It's on Vanes, not the prosecutors, to find her, and he says a friend is down in Florida looking.

On April 20 David Lynch e-mailed Nesbitt: "I think a direct clear written communication to Timmy would be appropriate, important and indeed overdue. I hope you agree."

Apparently she did not.

But Medill has nothing to say to Donald that would lift his spirits. The new director of the Medill Innocence Project is Alec Klein, and on his watch the project seems less interested in freeing the innocent than separating itself from the Protess era. "We put a little logo up, 'In Pursuit of the Truth.' That's what we're after," Klein told me. "The ends do not justify the means. We're not keeping score about exonerations. We want to teach students how to do things well and properly." Instead of turning over its findings to anybody, the project now posts them on its website. And it doesn't dawdle: results of the most recent investigation to appear on the site were posted after ten weeks of work—compare that to the three years the old Medill Innocence Project spent on Donald. The site boasts "thousands of pages of public documents Medill students obtained."

So why not simply post the entire Donald file online? That would require Klein, who doesn't like to speak Protess's name, to vouch for his casework. "We're not taking up any of his old cases," Klein told me. "You know, several of them are problematic. I've received some phone calls and e-mails about [the Donald] case and I've referred them to the previous instructor. I don't know anything about the case."

"To me, the M.I.P. are sending mix messages," Donald recently wrote Lynch. (Lynch forwarded the letter to Nesbitt.) "On one hand, they want everyone to believe they are commited to helping vindicate those who have [been] wrongly convicted. Then, on the other hand, they are refusing to hand over crucial information that could exonerate me. I'm very disappointed that it ended this way."

Correction: an earlier version of this column incorrectly described a Medill Innocence Project investigation as the project's most recent. While the investigation is the most recent for which results are posted on the project's website, there is a more recent investigation underway."