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Four years after arriving as Northern Illinois University president promising a new era of ethical leadership, Doug Baker said he would resign in the wake of a bombshell state watchdog report that alleged improper spending during his tenure.

Baker announced his resignation at Thursday’s board of trustees meeting and said he would leave at the end of the month, taking a six-figure severance with him. Trustees named Executive Vice President and Provost Lisa C. Freeman acting president, starting July 1 and serving until a permanent replacement is hired..

Baker continued to deny the report’s damning assertions — that administrators under his leadership routinely skirted ethics requirements to hire highly paid consultants, covered the consultants’ housing and travel expenses, and then kept them on staff for too long at lofty pay levels.

But Baker said he had reached the conclusion that the investigation, which was conducted by the Governor’s Office of Executive Inspector General, proved a “significant distraction” and he could no longer continue.

Baker said he recently approached NIU’s board chairman, John Butler, to discuss the leadership for the DeKalb-based university.

“The result has been that the university community has continued to be distracted by the allegations in the report,” Baker said in a statement. “Given the challenges we face and the hard work ahead, I simply couldn’t stand by and let this situation continue to fester.”

Baker will receive a one-time payment of $450,000, equal to a year of his salary, according to the terms of his transition agreement released by the university. In exchange for also resigning his tenured position in the College of Business, he also will receive a lump sum of $137,500.

Baker also will be paid up to $30,000 for his “reasonable, unpaid expenses for legal counsel” relating to his time at the university. He must vacate the presidential residence by July 31, according to the agreement.

Baker arrived at the DeKalb-based university in 2013 after a long career as a university faculty member and administrator in Washington state and Idaho. He replaced John Peters, who had been Northern Illinois’ president since 2000.

At the time of Baker’s hiring, Northern Illinois was embroiled in a series of scandals, including accusations that university police had mishandled an allegation of sexual assault by an officer, and that employees were selling scrap materials from university buildings and using the proceeds as a slush fund.

Baker struck a high-minded tone as he accepted the position.

“I want to have ethically inspired leadership at every level,” Baker told the board of trustees at the time. He added that he would not allow “distractions” to derail the university’s educational mission.

On Thursday, he made good on that promise.

The inspector general launched a probe into Northern Illinois’ hiring practices in 2014 following several anonymous tips. Illinois law requires state agencies to publicly bid out contracts for professional services from an independent contractor worth more than $20,000. But the report found that the university hired nine employees between June 2013 and May 2015, paying them all more than $20,000, but never solicited bids for those jobs.

Two of those workers each were paid more than $400,000 for 15 and 18 months of work, making them the third- and fourth-highest paid employees at the university, behind the head football coach and Baker, who had a five-year contract that paid him an annual base salary of $450,000. Another employee collected $23,000 for 30 days of work, the report found.

To do that, the report concluded, Baker and his top administrators cloaked their actions by deliberately assigning the employees the wrong classification — a designation ordinarily used for short-term, part-time workers and which does not require public bidding.

Additionally, the university spent tens of thousands of dollars to cover travel expenses and on-campus lodging for the five workers, the report stated.

In all, investigators wrote, Northern Illinois spent more than $1 million on these employees.

Students from Illinois pay almost $26,000 to attend Northern Illinois for a school year, including tuition, room, board and other fees. Out-of-state students pay more than $35,000.

Since Baker took office in 2013, “NIU has repeatedly misclassified high-level, highly paid consultants as affiliate employees, for the purpose of circumventing the Procurement Code’s requirements,” the report said.

“Ultimately, President Baker is responsible for mismanaging NIU’s resources,” the report concluded.

Greg Long, president of Northern Illinois’ faculty senate, said he was disappointed that Baker resigned.

Long noted that Baker and trustees had already implemented reforms before the report’s release — like eliminating the employment classification at issue — and that he felt many employees were prepared to move forward from the issue.

“Although hiring and reimbursement mistakes occurred, I believe they were unintentional and made in good faith,” Long said. In the end, he added, the criticism of Baker generated by the report would be hard to overcome.

“The president recognized that public perception was unlikely to change and that continued focus on the report would be a distraction to the university,” he said.

The head of the student government did not respond to a request for comment.

The report’s findings were released to university officials nearly a year ago but made publicly available only on May 31.

Investigators also accused Steven Cunningham and Celeste Latham, a former and a current human resources administrator, of wrongly classifying the five workers; and Doris Hooker Day, Baker’s executive assistant, of misusing her university credit card to pay one of those employee’s travel expenses.

Cunningham, who no longer works at the university, and Latham both denied wrongdoing, saying through their attorneys that they had recognized the problems with the hiring practices but ultimately followed their boss’ directives. Day declined comment.

The resignation is a setback not only for Northern Illinois, but also for an Illinois public university system that has been increasingly embroiled in controversy and under mounting financial strain amid the state’s two-year budget stalemate.

Baker previously said Northern Illinois has eliminated 50 academic majors, minors and certificate programs to cut costs. It has received about $74.7 million in state money for the past two years, compared with $91 million in 2015, the last year of regular funding.

Now, the university finds itself once again searching for a new president.

“President Baker arrived at a challenging moment for the university,” Butler said in a statement. “He brought fresh thinking to our campus, clarity to our mission and sharper focus to our efforts to prepare students for career success.”

drhodes@chicagotribune.com

Twitter @rhodes_dawn