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With a heartfelt farewell message, Assistant Seattle Police Chief Jim Pugel announced his retirement Thursday, ending a 31-year career in which he served a stint as interim police chief during one of the most tumultuous times in the department’s history.

Pugel’s retirement, effective Monday, comes only months after he sought to position himself for the job of permanent chief.

But his chances appeared to dwindle after new Mayor Ed Murray took office in January, defeating Mike McGinn, who had appointed Pugel as interim chief last April.

As Murray launched a search for a new chief, he replaced Pugel in January with a new interim chief, Harry Bailey, and then Pugel found himself forced with the choice of retiring or taking a demotion to captain.

Pugel, 54, became the third assistant chief to choose to retire since Murray became mayor and vowed to make federally mandated police reforms a top priority.

Pugel and the two other assistant chiefs — Clark Kimerer and Mike Sanford — held key command-staff roles as the department came under scrutiny in recent years over excessive use of force and biased policing. In 2012, the city entered into a landmark settlement agreement with the U.S. Department of Justice to adopt reforms.

While serving as interim chief, Pugel said he planned to pursue the permanent position, putting him at odds with Murray’s condition that the interim chief not seek the permanent job.

Murray said he wanted an interim chief who could make decisions without having his motivations questioned. Bailey said he wouldn’t apply for the permanent post, which Murray is seeking to fill by the end of May.

Pugel returned to the assistant chief rank, with a special assignment to work on the department’s ongoing effort to reduce harm in drug policing and other enforcement.

But notably, Pugel was not listed in Bailey’s newly formed command staff. He was given the choice to retire or to take a demotion to his civil-service rank of captain, according to a source familiar with the matter.

At some point, Pugel took a leave while negotiating the terms of his departure.

It is unclear whether Pugel still plans to pursue the permanent job, which is widely expected to go to someone outside the department.

Pugel could not be reached for comment Thursday and did not answer the question in his lengthy, emotional and memory-filled message addressed to his “Seattle Police Family Members.”

“It is with mixed emotions that I am announcing my retirement from the Seattle Police Department at the end of this month,” he wrote. “There is sadness, because I will not be working daily with all of the great civilian and sworn employees of the Seattle Police Department in making Seattle even safer than it is today.

“Happiness, because after 31 years in policing, it is time to move into other areas of improving how police services are delivered,” he added. “Curiosity, because I will be able to watch you within the department accept the opportunities to continue moving the profession and the department forward in innovative and constitutional ways.”

Pugel’s retirement caps a remarkable career.

The Seattle native and University of Washington graduate started as a volunteer reserve police officer in 1981. He was hired as a full-time officer in January 1983 and promoted to sergeant seven years later.

He supervised a patrol squad at the East Precinct, then worked at the Basic Training Academy before being promoted to lieutenant in 1994. He was a watch commander and an operations lieutenant in the East Precinct before taking command of the sexual-assault unit.

In 1999, Pugel was promoted to captain of the West Precinct.

“I will always remember being assigned as the West Precinct commander seven months before what was initially described to me as ‘ … a small, international trade fair called the WTO,’ ” Pugel wrote in his farewell message, referring to the 1999 World Trade Organization meeting in Seattle that erupted in riots.

In 2000, Pugel became an assistant chief. As commander of the department’s investigation division before he was named interim chief, he earned wide praise for the unit’s work on high-profile investigations.

Early in his tenure as interim chief, Pugel struck a cooperative stance on police reforms. He said he anticipated having a good working relationship with the federal monitor, Merrick Bobb, who is overseeing the settlement agreement.

Bobb praised Pugel for pushing reforms, although in a stinging progress report late last year Bobb sharply criticized the pace of change, highlighting resistance by some in the top ranks.

In response, Pugel demoted two assistant chiefs, Nick Metz and Dick Reed, to their civil-service ranks of captain. But Pugel kept Kimerer and Sanford on his command staff, a decision that some observers saw as stemming from old loyalties.

Bailey restored Metz to the rank of assistant chief and ushered out Kimerer and Sanford, a clear sign Pugel’s star had faded.

More recently, Pugel found himself locked in a dispute with the city as he denied that, as interim chief, he tentatively approved the reversal of misconduct findings against six officers. Bailey cited Pugel’s purported action as a basis for giving final approval to the controversial reversals.

On Thursday, Bailey issued a statement on behalf of the Police Department congratulating Pugel on his retirement.

“SPD hopes that in his retirement, Chief Pugel will continue to champion the cause of harm reduction, and that he will have a bit more time to root for his Washington Huskies — especially the rowing program — where he rowed as an undergrad, and now as a member of the Women’s’ and Men’s Rowing Board,” Bailey wrote.

As recently as 2010, Pugel was one of 11 semifinalists for the job of police chief after Gil Kerlikowske stepped down in 2009 to become the nation’s drug czar.

Deputy Chief John Diaz was ultimately chosen.

When Diaz retired and then-Mayor Mike McGinn decided to appoint Pugel as interim chief, Diaz cited Pugel’s work on the innovative Law Enforcement Assisted Diversion program, in which officers can divert low-level drug dealers and addicts into treatment instead of taking them to jail.

Steve Miletich: 206-464-3302 or On Twitter @stevemiletich