Metra's board spent about 10 months screening 40 candidates during a nationwide search before selecting Los Angeles native Alex Clifford to be the commuter rail agency's CEO in February 2011.
On Friday, after several months of closed-door negotiations over an exit strategy, board Chairman Brad O'Halloran announced that Clifford was resigning, taking a buyout package that could cost Metra as much as $740,000.
Officials wouldn't immediately speculate on what's next, but if past is precedent, Metra's board will soon launch a search for a new leader for one of the nation's largest commuter rail agencies, providing 300,000 trips a day on 11 lines.
Experts say Metra's board members will need to hire someone who has both the skill to run a major railroad and the savvy to navigate Illinois' Byzantine politics.
Clifford is walking away from the agency with eight months left on his $252,500-a-year contract. Lengthy negotiations led to a separation agreement that gives him a $442,237 buyout covering the remainder of his salary, a severance payment, health insurance and relocation and attorney fees.
Clifford also could collect an additional payout of up to $300,000 if he cannot find another job within 13 months, according to the agreement.
The deal was approved by Metra's board 9-1 with one "present." Only McHenry County representative Jack Schaffer, who was on the board when Clifford was hired, voted no.
"In 1983 when Metra was created, the idea was — I was in the room — (to have) a transit professional with a politically appointed oversight board," said Schaffer, a state legislator at the time. "Apparently, we want to go a different direction now. I don't."
Schaffer added: "There's a dramatic difference of opinion as to who runs the shop" at Metra. "No strong executive director — the chairman calls the shots."
Clifford left Friday's meeting before the announcement of the settlement and could not be reached for comment.
O'Halloran, who took over as Metra chairman in November, read a statement saying there were "differences of opinion … with respect to what we need (in) leading this organization."
Metra's board members are political appointees, subject to leaders in the six-county region that Metra serves.
O'Halloran also alluded to the importance that politics plays in getting funding and official support for Metra, and he hinted that he and Clifford didn't see eye to eye.
"The board believes it's critical that Metra move in a different direction, one built on finding a new consensus in Springfield and Washington, (and) develop new resources to serve our taxpayers and our communities," O'Halloran said.
Steve Schlickman, former executive director of the Regional Transportation Authority and now head of the Urban Transportation Center at the University of Illinois at Chicago, said the chairman of a major public agency like Metra needs to have a CEO with whom he is comfortable.
"Obviously, that was not the case in this situation unfortunately," Schlickman said.
Schlickman and other experts agree that Metra needs a transportation professional who is adept at politics.
Clifford brought fresh ideas to Metra, but that's often not welcome to the elected establishment, said DePaul University transportation expert Joseph Schwieterman.
"I think its tough for an outsider to win the favor of the politically connected boards, and (Clifford) may have fallen victim to the treacherous politics," Schwieterman said.
Schwieterman cited CTA President Forrest Claypool as someone who runs a major transit agency but who also has long been part of the region's political structure.
"It may take a political whiz to wrangle more funds out of Springfield and Washington," Schwieterman said.
As one of his first acts at Metra, Clifford brought in a well-known professional railroad consultant, George Avery Grimes, to help him run the agency. Clifford had run a metropolitan bus agency in Los Angeles.
"Alex did the hard lifting to fix the financial and ethical problems, provided transparency to the public, and improved service quality. He did it in record time. Now he's been sent packing," said Grimes, who received a hefty contract for his work.
"In my opinion, this is a travesty for Metra," Grimes said. "It sends a terrible message to Metra's employees and talented, ethical public servants everywhere."