Shanahan Withdraws as Defense Secretary Nominee, Mark Esper Named Acting Pentagon Chief

President Trump on Tuesday withdrew the nomination of Patrick M. Shanahan to be the permanent defense secretary, leaving the Pentagon in transition at a time of escalating tensions with Iran and questions about the role of the military at the border with Mexico.

Mr. Shanahan, who had been serving as the acting defense secretary, announced his resignation as a routine F.B.I. background investigation, conducted on all cabinet nominees, was continuing because of Mr. Shanahan’s divorce. Mr. Shanahan’s ex-wife had accused him of punching her in the stomach, which Mr. Shanahan has denied. He said that his ex-wife started the fight, and his spokesman said that she was arrested and charged with domestic violence, charges which were eventually dropped.

Mr. Trump named Mark T. Esper, the secretary of the Army and a former Raytheon executive, to take over as acting secretary of defense. He did not say whether Mr. Esper would be nominated for the permanent position.

In a Twitter post, the president said the withdrawal was the decision of Mr. Shanahan, who has served for six months as acting defense secretary. But it is the president’s prerogative to withdraw the nomination.

According to court documents viewed by The New York Times, in 2011 Mr. Shanahan’s son, who was 17 at the time, hit his mother repeatedly with a baseball bat, and she was hospitalized. The next day, Mr. Shanahan flew from Seattle to Florida and stayed with his son in a hotel room for several days before his son turned himself into the authorities.

“I would welcome the opportunity to be secretary of defense, but not at the expense of being a good father,” Mr. Shanahan said in a statement on Tuesday afternoon.

In an interview with The Washington Post published Tuesday, Mr. Shanahan said that “bad things can happen to good families.” He called the episode “a tragedy,” and said that dredging it up publicly “will ruin my son’s life.”

During his tenure, Mr. Shanahan was criticized for slighting Lockheed Martin, Boeing’s chief competitor, for its mismanagement of the F-35 Joint Strike Fighter, an aircraft that is years behind schedule and millions of dollars over budget.

He was widely viewed as acquiescing to the White House and other government officials, including John R. Bolton, the national security adviser, and Mike Pompeo, the secretary of state. As he defended the president’s proposal to create a Space Force in the military, Mr. Shanahan famously said that the Pentagon would not be viewed as the “Department of No.”

Before Mr. Trump plucked him to be the acting secretary, Mr. Shanahan was a deputy secretary of defense, brought on to make the bureaucracy operate more like a business. His reputation at Boeing was as someone who could meld technical details with a broad vision. At the Pentagon, he was known for digging into the details. He held five-hour meetings about F-35 fighter jets on some Saturdays.

Earlier this year, the defense department’s inspector general conducted an ethics investigation into whether Mr. Shanahan “repeatedly dumped” on Boeing’s competitors, and ultimately cleared him of the allegations. Once that hurdle was removed, Mr. Trump nominated him to be the next secretary.

Mr. Trump’s decision not to move ahead with Mr. Shanahan is the latest evidence of the difficulty that the president has had in permanently filling the top jobs in his administration.

The president also has an acting chief of staff at the White House and an acting secretary of homeland security.

Mr. Esper, a top lobbyist for Raytheon and an executive at the U.S. Chamber of Commerce, has a long history of ties to lawmakers on Capitol Hill, where he worked as an adviser to Bill Frist, the former Senate majority leader, and various committees with jurisdiction over foreign policy and national security.

Besides Mr. Esper, who was confirmed as secretary of the Army in November 2017, officials said that Mike Pompeo, the secretary of state, and Richard V. Spencer, the secretary of the Navy, are on the short list for defense secretary.

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