The news came at Friday morning's Metra board meeting. Clifford was recruited from Los Angeles in 2011 to succeed Phil Pagano, who committed suicide in 2010 after it was discovered that he padded his vacation time.
Pagano stood in front of a Metra train the day he was about to be fired for pocketing nearly half a million dollars in unapproved vacation pay.
Alex Clifford was hired on a February day in 2011 when a big blizzard smacked Chicago. His leadership at Metra since was considered stormy by some, professional by others. Clifford resigned after reaching a severance agreement with a board that did not want to keep him - with the exception of one member who argued that Clifford did bring needed reform to the commuter rail agency.
So it was Clifford's job to cleanse Metra of Pagano-era patronage and favoritism, and some think he did well toward that end. But Clifford's opponents - who grew in number - found the new boss to be abrasive, autocratic, unaware or unwilling to work with politicians who have say-so over Metra funding.
Clifford also took heat from bringing in a high-priced rail consultant, and although it was the board that approved them, Clifford presided over the biggest fare hikes in Metra's history. He left his office without comment Friday. He departs seven months before his contract expires with a severance package of $442,000.
"We hope [customers] don't notice a difference. It should be seamless. Customer service was important before. It still is. Our customers are still important to us and we don't think they'll notice a change," said Metra spokesman Mike Gillis.
Metra's board chairman has declined comment on the Clifford departure. Clifford could receive another $300,000 on top of his severance if he's unable to find a new job within the next 13 months.