Metra officials Friday voted to give CEO Alex Clifford a $442,000 severance package and accept his resignation.
Clifford's fate at the commuter rail agency had been the subject of closed-door meetings of the board this spring.
In remarks prepared for Friday's meeting of the Metra board, Chairman Brad O'Halloran of Orland Park addressed Clifford's severance package but provided few specifics about why the CEO was resigning.
"It is generous, but reflects the recognition that Mr. Clifford uprooted his family to take this position during a difficult time for the agency," the remarks read. "At the same time, the board believes it is critical that Metra moves in a different direction -- one built on finding a new consensus in Springfield and Washington to develop new resources to serve our passengers and our communities."
The board voted 9-1 to accept Clifford's resignation.
The lone "no" vote was from Jack Schaffer of Cary, who praised the job Clifford was doing and said O'Halloran had a "very, very serious philosophical difference" over who should be running Metra.
"We just have a chairman who wants to run the place," Schaffer said.
Clifford took over as Metra CEO in February 2011 following the suicide of former executive director Phil Pagano. Pagano was later found to have cheated Metra out of about $500,000.
Clifford's contract was set to run through February, and his salary was $252,500 a year.
In addition to Clifford's salary through February, the Metra board agreed to pay him for six additional months, then pay any difference between his Metra salary and earnings from any future job through Aug. 11, 2015, according to a copy of the separation agreement supplied by Metra.
Metra also will pay $35,243 for unused vacation days, $21,971 for unused sick days, and reimbursement for Clifford's pension contributions because he will not qualify to collect benefits, according to the agreement.
Metra also will pay up to $78,000 to reimburse Clifford for selling his home and relocating and up to $75,000 for Clifford's legal costs related to his negotiations with Metra.
In his statement, O'Halloran said Metra agreed to the terms to avoid legal entanglements.
"It became clear that there were differences of opinion over his (Clifford's) legal rights under his contract," O'Halloran said.
"It therefore became important to resolve such legal disputes so that Metra can move forward with a clean slate, and avoid wasting time and money on attorneys."
During Clifford's tenure, controversial fare raises were approved and a hiring probe by the Illinois Office of the Executive Inspector General began.
Stephen Schlickman, executive director of University of Illinois at Chicago's Urban Transportation Center, praised Clifford but said it's important that the board and CEO see eye to eye.
"While Alex Clifford has made great strides in reforming Metra, it is very important that the Metra board of directors and the executive director have a good working relationship in order to ensure that they are jointly best serving the interest of the Metra riders and the taxpayers of the state who are subsidizing Metra operations," said Schlickman, a former executive director of the Regional Transportation Authority.
A timetable or process to fill the CEO job hasn't been set, Metra spokesman Michael Gillis said. In the meantime, the agency's two deputy directors -- Don Orseno and Alex Wiggins -- will handle Clifford's former duties.
• Daily Herald staff writer Mick Zawislak contributed to this report.