Early in his first administration, President Trump noted the general’s “brilliance and fortitude.” And then the president got angry.

Senators Lindsey Graham and Tom Cotton said that the former Trump aides faced continuing threats from Iran and that the decision could affect how current officials do their jobs.

The second Trump White House is starting out with a remarkable degree of conflict among different individuals, constituencies and worldviews.

Even Republicans who once said violent rioters should be prosecuted to the fullest extent of the law declined to criticize the presidential clemency for violent offenders, saying it was time to move on.

The affable traditional conservative from South Dakota is the first new chief of the Senate G.O.P. in nearly two decades. He will confront a challenge managing President-elect Donald J. Trump’s expectations.