WASHINGTON — After months of unexplained delays, Acting Defense Secretary Patrick Shanahan stepped down Tuesday before his formal nomination ever went to the Senate, citing a “painful” family situation that would hurt his children and reopen “wounds we have worked years to heal.”

President Donald Trump tweeted that Shanahan would not be going through with the nomination process, which had been delayed by an unusually lengthy FBI background check, “so that he can devote more time to his family.”

Trump said that Army Secretary Mark Esper would be the new acting Pentagon chief.

“I believe my continuing in the confirmation process would force my three children to relive a traumatic chapter in our family’s life and reopen wounds we have worked years to heal,” Shanahan said in a statement. “Ultimately, their safety and well-being is my highest priority.”

Shanahan, a former Seattle resident and onetime Boeing executive, was interviewed about the family matter by The Washington Post, which published the interview Tuesday, shortly before Trump tweeted that his nomination would not go forward.

In the interview, Shanahan spoke about the circumstances surrounding his 2011 divorce and said he didn’t want to drag his children through the experience again.

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“Bad things can happen to good families … and this is a tragedy, really,” Shanahan told the Post.

In 2010, his wife was arrested after punching him in the face at their home in Seattle, and his son was arrested after an incident in 2011 in which he hit his mother with a baseball bat, according to court documents.

Details of the incidents have started to emerge in media reports about his nomination, including a USA Today report Tuesday about the incident in 2010.

In his statement, Shana­han said he asked to be withdrawn from the nomination process and he resigned from his previous post as deputy defense secretary. He said he would work on an “appropriate transition,” but it wasn’t clear how quickly he will leave the job.

The post atop the Pentagon has not been filled permanently since Gen. James Mattis retired in January after policy differences with Trump. Trump announced in May that he would nominate Shanahan, who has been leading the Pentagon as acting secretary since Jan. 1, amid questions about his lengthy work history as a Boeing executive and persistent questions about possible conflicts of interest.

The Defense Department’s Inspector General cleared Shanahan of any wrongdoing in connection with accusations he had shown favoritism toward Boeing during his time as deputy defense secretary, while disparaging Boeing competitors.

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In Shanahan’s tenure at the department he’s had to deal with a wide array of international hot spots, ranging from missile launches by North Korea to the sudden shift of military ships and aircraft to the Middle East to deal with potential threats from Iran.

Shanahan, 56, had extensive experience in the defense industry but little in government. In more than four months as the acting secretary, he focused on implementing the national-defense strategy that was developed during Mattis’ tenure and emphasized a shift from the resources and tactics required to fight small wars against extremist groups to what Shanahan calls “great power” competitions with China and Russia.

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

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

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.

In addition to Esper, officials said Secretary of State Mike Pompeo and Richard Spencer, the secretary of the Navy, are on the shortlist for defense secretary.

At the Pentagon, officials were internally discussing that a routine FBI investigation for Cabinet nominees was dragging on for Shanahan because of his divorce, which included an allegation made by his ex-wife — and denied by Shanahan — that he punched her in the stomach.

Shanahan climbed the ranks at Boeing over more than two decades, becoming vice president and general manager of the corporation’s commercial-airplane program in 2008. He was known for his ability to turn around sputtering projects worth billions of dollars, such as the aerospace giant’s delayed 787 Dreamliner program. By 2010, Shanahan was earning more than $935,000 annually in salary and bonuses, court records show.

But there was turbulence in Shanahan’s personal life with Kimberley, his wife of 24 years. Shanahan and two of his children interviewed by the Post said she was growing more erratic.

Things culminated with a physical dispute on Aug. 28, 2010. According to Patrick Shanahan, the incident came after an argument with Kimberley Shanahan about their oldest child.

A Seattle police report obtained through a public-disclosure request by USA Today alleges police arrived at the Shanahans’ Laurelhurst home just after 1 a.m. to find Patrick Shanahan sitting on the sidewalk with another officer, with an apparent black eye and bloody nose. The officer said he saw a pile of clothes in the driveway when he approached Kimberley Shana­han, who the officer said smelled of alcohol and appeared to be intoxicated. Asked if she had been drinking, the then-47-year-old said she had not, according to the report.

The report indicates Patrick Shanahan had been drinking, but the report does not indicate whether he was intoxicated.

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In a handwritten statement to police that night, Patrick Shanahan said that his wife tried to “provoke him” into an argument and struck him in the head. He said she started throwing clothes from his closet outside.

Shanahan said his wife then tried to disconnect a propane tank from an outside barbecue but was unable to do so. She then grabbed some paper towels and set fire to them with a lighter. Shanahan grabbed them from her, he wrote, stating that his wife then tried to set fire to his shirt.

Shanahan said he then went outside and was loading clothes into his car when his wife approached again and struck him several times. She told officers that he punched her several times in the stomach. Patrick Shana­han denied he hit his wife. An officer noted in the report that she had blood on her forearm.

Seattle police listed Kimberley Shanahan as the aggressor in the incident and eventually arrested her. The case was referred to the Seattle City Attorney’s Office, which charged her with misdemeanor assault. A judge in Seattle Municipal Court issued a no-contact order against her on Aug. 30, 2010, according to court records obtained by The Seattle Times. The city attorney’s office dismissed the case on Oct. 29, 2010, citing “proof” problems, and lifted the restraining order. Records show the couple divorced in 2011.

Kimberley Shanahan won custody of their three children and moved to Florida. Patrick Shanahan remained in Seattle, and the couple’s eldest daughter soon would rejoin him to attend college.

Shortly after midnight on Nov. 23, 2011, Kimberley Shanahan and their son William, then living near Sarasota, Florida, got into “a verbal dispute” over her suspicion that the 17-year-old was in a romantic relationship with a 36-year-old woman, according to a police report.

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According to police, just after 1:30 a.m., William hit his mother on the head and torso with a baseball bat and left her “to lie in a pool of blood,” and fled, police said.

The younger brother called 911 from a neighbor’s phone, according to police records.

Kimberley Shanahan had a fractured skull and elbow, according to court and police records, and required surgery.

After William contacted his father, Patrick Shanahan flew to Florida, according to court records and documents provided by the Pentagon, and arranged to stay with William in a hotel.

Derek Byrd, head of a well-known Sarasota defense firm hired by Patrick Shanahan to represent his son in the criminal case, said in an interview that the elder Shanahan acted appropriately by not contacting police until his son could consult a defense attorney, a process that was delayed by the Thanksgiving holiday.

Byrd also said that Patrick Shanahan was not aware that police were searching for his son in the days after the attack.

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Another attorney from the firm contacted the detective handling the case and said he would arrange for William Shanahan to turn himself in, which he did several days later.

The judge declined to release William Shanahan, calling pictures of the crime scene “horrendous.”

He was initially charged with two felonies, aggravated battery and tampering with a victim, and faced up to 15 years in prison.

Shanahan sent his ex-wife’s brother a memo arguing that his son had acted in self-defense.

“Use of a baseball bat in self-defense will likely be viewed as an imbalance of force,” Shanahan wrote. “However, Will’s mother harassed him for nearly three hours before the incident.”

In an hourlong interview Monday night at his apartment in Virginia, Shanahan, who has been responding to questions from The Washington Post about the incidents since January, said he wrote the memo in the hours after his son’s attack, before he knew the full extent of his ex-wife’s injuries. He said it was to prepare for his son’s initial court appearance and that he never intended for anyone other than his son’s attorneys to read it.

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Kimberley Shanahan, who has since changed her name to Kimberley Jordinson, has not responded to repeated efforts by reporters to contact her.

Patrick Shanahan’s memo also alleged a history of substance abuse, emotional abuse and violent tendencies by Kimberley Shanahan. It casts his ex-wife as the instigator in conflicts with him and their children.

Kimberley Shanahan disputed those characterizations in a court filing.

“I have always been a very loving and dedicated mom,” she wrote in the filing responding to the memo, “and I have never emotionally abused any of my children for any period of time.”

Prosecutors charged William as an adult with one felony: aggravated battery with a deadly weapon. He pleaded down to a third-degree felony, and in 2012, a state prosecutor agreed to curtail the length of the sentence and probation.

William was ordered to spend 18 months at a Florida Sheriff’s Youth Ranch and sentenced to four years’ probation. Both penalties were later reduced.

The next year, in 2013, William enrolled at the University of Washington, according to his LinkedIn page. His father had recently joined the university’s board of regents. Patrick’s father, Michael, had served as police chief for the university for more than two decades.

William graduated last June with a degree in political science, a university spokesman said.

Kimberley Shanahan lost custody of the couple’s youngest child in 2014, when a judge wrote that she had “engaged in abusive use of conflict that is seriously detrimental” to the child. According to multiple accounts, she is now estranged from all three of her children. At his last confirmation hearing, to become deputy secretary of defense in June 2017, all three children were sitting behind Patrick Shanahan.