Brad O'Halloran is calling it quits at Metra.



The Chairman of the Board for the embattled transportation agency told NBC Chicago exclusively on Thursday that he is resigning his post effective immediately so that Metra can get back on track in the wake of a growing scandal.



"It is with mixed feelings that I step down," O'Halloran writes in his resignation letter to the Cook County Commissioners responsible for his appointment. "Unfortunately, a media and political frenzy has been stirred up, primarily related to the Alex Clifford separation agreement. I have come to the sad conclusion that, so long as I am Chairman and a member of the board, the truly critical issues facing Metra will be left aside while the focus remains on the next big headline or attention-grabbing quotation."

In a joint statement, Metra Deputy Executive Directors Alex Wiggins and Don Orseno thanked O'Halloran for his service.

"Metra’s staff will continue to work with our Board members and focus on our agency’s mission to provide the riders and taxpayers of Northeast Illinois with high-quality, safe, affordable and reliable commuter rail service," they said. "Our customers should expect no change."



O'Halloran becomes the third board member to resign in the wake of a payout scandal that leads all the way back to Illinois Speaker of the House Michael Madigan. But as he departed, he raised issues with the way the story has played out up until now and the character of former CEO Alex Clifford.



"The facts, I believe, keep getting distorted," he said. "No one wants to really look at the facts. They want to look at the sensationalism that’s out there. ... I have to think what’s best for Metra, not what’s best for Brad O’Halloran. And what’s best for Metra, is now, for me to stop down."



In June, Clifford resigned his post as Metra CEO and received a significant buyout. He was paid $442,000 in severance with an opportunity to make another $300,000 if he fails to find a new job in the next 13 months. Because of a confidentiality clause in that agreement, some decried the payout as political hush money.

After questions were raised about the package, a Clifford memo, and later testimony before the RTA Board, alleged pressure he said he had received from Illinois politicians, including Madigan, to promote political allies and increase the pay of others.



"In the last year I have refused on several occasions to make employment-related decisions based upon political sponsorship or support of an employee or applicant by members of the Illinois legislature," Clifford wrote in the memo.



He said O'Halloran and former Metra chief Larry Huggins had criticized his conduct, and alleged they had faulted him for not playing ball with insiders in Springfield. But O'Halloran denies those events and disputes many of the claims Clifford has made since June.



"That's absolutely untrue," O'Halloran said about the alleged conversation in which he supposedly scolded Clifford for not agreeing to deal with Madigan. "Did that conversation ever happen? No."



In his letter of resignation, the Metra Chairman said Clifford had "misrepresented, or outright invented supposed conversations he claims to have had with me."



“I have never asked anyone at Metra, including Mr. Clifford, with respect to any job whatsoever, or any contract whatsoever,” he told NBC Chicago. "Never went to anyone in the agency and said would you consider this individual and not this individual, or would you look more favorably at this organization as opposed to that organization. Never happened."



Indeed, O’Halloran notes it was he who advocated an independent investigation of the Clifford allegations. The Metra board was on the verge of hiring former federal prosecutor Patrick Collins to conduct the inquiry, when Collins backed out, citing an unspecified conflict-of-interest.



O'Halloran insisted he had never witnessed the politicized agency which Clifford described.



"I didn’t see any of that," he said. "I saw hard working men and women."



Clifford had pointed to a March 2012 incident where he said Rep. Luis Arroyo made clear he wanted a deputy director position filled with a candidate recommended by the legislative Latino caucus. He said Huggins "told me he agreed with Representative Arroyo's request."



At the same time, Clifford said he was made aware that House Speaker Madigan wanted a Metra employee named Patrick Ward, a personal associate, to receive a pay raise. He said Madigan also requested that another individual receive a job with Metra.



"Clifford's allegations in a memo have been treated as gospel," O'Halloran said. "No one's really looked into each of his allegations in the same way they've looked at the separation agreement."

He repeated his insistence, that he has no connection to Madigan or his considerable political might.



"I've never had a conversation with Mr. Madigan. I've never met Mr. Madigan. I've never talked on the phone with Mr. Madigan," he said.



Ironically, in his resignation letter, O’Halloran did make references to political forces in Illinois. Repeating his contention that a formal investigation of the entire affair was needed, he said, “I know some powerful people in this state must be breathing a sigh of relief that Mr. Collins is not able to lead this effort.”



"While I have been taking the heat,' he wrote, "it seems the powerful politicians Mr. Clifford accused, escaped the same level of criticism.">



While O’Halloran would like to correct what he says are errors in the narrative, he says he wouldn't change his actions. He said he would still involve the office of the inspector general in the political allegations and he still would have agreed to give Clifford a severance package.



"We wanted the agency to move forward and that's how everyone saw it at the time," he said. “It was bad option A versus bad option B.” And he repeated his contention that fighting a potential Clifford lawsuit would have been more expensive than the settlement.



O'Halloran, who is also stepping down as a Village of Orland Park Trustee, says he is looking forward to moving on from this crisis, which he conceded has been difficult on his family.



"You know, I look forward to the next chapter of my life, and I wish everyone well."