Either way, it has been a tough week for Mr. Kelly, to say the least.
“Ya think?” said the former defense secretary Leon E. Panetta, a onetime boss to Mr. Kelly, who retired as a four-star Marine general. “I worry about John. Even he has admitted it’s probably the toughest job he’s ever had. And I really do think sometimes, particularly with this president, you’re fighting on so many fronts it’s tough not to have that job wear on you.”
But Mr. Kelly’s long service to his country as a Marine did not necessarily prepare him for the job of White House chief of staff, added Mr. Panetta, who had that post himself under President Bill Clinton. “It comes to that political judgment,” he said. “You’ve got to have your antenna up. You’ve got to be able to anticipate where the hot spots are.”
This week was not the first time that Mr. Kelly did not seem to foresee hot spots. When he took the White House job last summer, he was seen by many as a mature figure who could impose order on a chaotic building. By most accounts, he has indeed created a more organized operation. But he has also generated repeated furors with words and deeds.
He engaged in a heated back-and-forth with an African-American Democratic congresswoman, distorting statements she had made at a ceremony they both attended. He opined that the Civil War resulted from “the lack of an ability to compromise.” He said that Mr. Trump had not been “fully informed” about border issues as a candidate and had since “evolved,” drawing a public retort from the president.
Mr. Kelly generated further heat this week when he dismissed many of the more than one million immigrants who were brought to the country illegally as children but who did not apply for the protection of an Obama-era program that Mr. Trump ordered ended next month. Some of them “were the people that some would say were too afraid to sign up, others would say were too lazy to get off their asses, but they didn’t sign up,” he told reporters.
Mr. Kelly at first came to the defense of Rob Porter, the White House staff secretary, who resigned in the face of allegations of spousal abuse. “Rob Porter is a man of true integrity and honor, and I can’t say enough good things about him,” Mr. Kelly said. “He is a friend, a confidant and a trusted professional.”
As outrage grew over a photograph showing an ex-wife of Mr. Porter with a black eye, Mr. Kelly issued a new statement. “I was shocked by the new allegations released today against Rob Porter,” he said. “There is no place for domestic violence in our society.” But he added: “I stand by my previous comments of the Rob Porter that I have come to know since becoming chief of staff and believe every individual deserves the right to defend their reputation.”
Mr. Porter’s case raised questions about what Mr. Kelly knew and when. The White House was informed as far back as August that Mr. Porter’s security clearance was being held up because of domestic allegations. Mr. Kelly has known about the allegations at least since last fall, according to officials who asked not to be named.
Raj Shah, a White House spokesman, said on Thursday that Mr. Kelly was not “fully aware” of the details until this week. Mr. Shah also insisted that Mr. Trump remained behind Mr. Kelly. “The president has confidence in his chief of staff,” he said.
One official insisted that there was minimal knowledge in the White House about Mr. Porter’s troubles. The official said that Mr. Kelly felt misled by Mr. Porter’s account of what had happened. A friend of Mr. Kelly’s said he had learned the details of Mr. Porter’s situation only an hour before suggesting he resign.
But White House officials said privately that the president was frustrated with both Mr. Kelly and the White House communications director, Hope Hicks, who in recent weeks has been dating Mr. Porter. Ms. Hicks was one of those rallying the White House to Mr. Porter’s defense when the allegations first surfaced in The Daily Mail.
Two people close to the situation said Mr. Kelly had strongly urged Mr. Porter to remain in his job. But a third person denied that, saying that Mr. Kelly had suggested to Mr. Porter on Tuesday night that he should resign. All three agreed that Mr. Kelly never demanded the resignation.
Mr. Kelly seemed determined to smooth concerns among staff members who were bewildered by the initial reaction to the allegations against Mr. Porter.
In a memo to the staff on Thursday night, Mr. Kelly wrote, “While we are all processing the shocking and troubling allegations made against a former White House staffer, I want you to know that we all take matters of domestic violence very seriously. Domestic violence is abhorrent and has no place in our society.”
Friends and associates noted that with Mr. Kelly’s lack of experience in Washington politics, he may not have been attuned at first to how the domestic abuse allegations against Mr. Porter would be perceived.
Mr. Porter was also a favorite of Mr. Kelly’s and viewed as one of the most competent members of an often dysfunctional White House team. Some friends expressed concern that Mr. Kelly had changed with his association with Mr. Trump and grown too insulated in the White House bubble.
Mr. Kelly has previously played down accusations against someone he believed served a greater goal. He appeared as a character witness in a 2016 court-martial of a Marine colonel accused of sexually harassing two female subordinates. Mr. Kelly praised the colonel as a “superb Marine officer.”
Mr. Kelly has spent much of his six months trying to clear out the White House of staff members he viewed as problematic, and colleagues have credited him with reducing internal feuding as a result. But even those efforts have caused him trouble.
He pushed out Omarosa Manigault Newman, the former reality show star who had been given a White House post, for what one White House official called misuse of government cars. In an interview on “Celebrity Big Brother” on CBS that aired on Thursday, Ms. Manigault Newman exacted some payback by describing a chilling White House. “I was haunted by tweets every single day, like what is he going to tweet,” she said.
She added that she tried to intervene but was blocked. Now that she is gone, she said, “I’d like to say it’s not my problem, but I can’t say that because, like, it’s bad.” Will everything be O.K., she was asked. “No, it’s going to not be O.K.,” she said. “It’s not.”
Mr. Shah dismissed her comments. “Omarosa was fired three times on ‘The Apprentice,’ and this is the fourth time we let her go,” he said.
But most attention on Thursday focused on Mr. Kelly and his handling of the charges against Mr. Porter.
“I have lost all confidence in him as chief of staff,” Evan Siegfried, a Republican strategist, said on MSNBC. “He’s becoming a distraction. He says things that are absolutely outrageous, and then he does things in the case of Rob Porter that are morally despicable.”
Representative Nydia Velazquez, Democrat of New York, wrote on Twitter that the Porter case was “part of a culture of misogyny at the #WhiteHouse.”
Republicans were not so quick to throw Mr. Kelly overboard, even as they questioned his judgment.
“General Kelly has done an extraordinary job as chief of staff to President Trump,” Senator John Kennedy, Republican of Louisiana, said on CNN. “I think he’s a good man. And sometimes good people make bad decisions. It doesn’t mean they’re bad people. It means they’re human.”
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