When the White House summoned the Pentagon’s top civilian leader to consider a possible military strike against Iran, two men answered the call: Patrick M. Shanahan, the acting defense secretary who had just announced he would step down amid revelations of family violence, and Mark T. Esper, the Army secretary slated to replace him, who had no formal standing to be in the room.

The arrival on Thursday of the two men at the White House, neither of whom came with the Senate’s imprimatur to sit at the table, brought into sharp relief the perils of a civilian leadership void that President Trump has tolerated at the Pentagon for more than half a year since Jim Mattis resigned as defense secretary. 

The end result — an 11th-hour reversal of a military strike that could have sparked an open conflict with Iran — fed into the fears of those who saw Mattis as a bulwark against a process that could leave matters of war and peace up to Trump’s last-minute whims and his interactions with cable news commentators. The deliberations over how to respond to Iran’s downing of an unmanned U.S. drone highlighted the absence of a top Pentagon civilian leader armed with the experience and status necessary to influence the commander in chief.   

“In the end this is a human process,” said Leon Panetta, who served as defense secretary and CIA director for President Barack Obama. “What human beings tend to do is they make judgments about people who are at the table, and whether or not they have the strength and the position and the knowledge and the experience to be able to voice their opinions.” 

“If they know that somebody is acting,” Panetta said, “if they know that somebody is just there on a temporary basis, then mark my words: There is an automatic assumption that what they say doesn’t carry a lot of weight.”

Signs have emerged that the crisis with Iran has possibly been a wake-up call for the White House about the need to install a permanent leader at the Pentagon quickly, despite Trump’s predilection for acting officials. After urging from impatient Republican lawmakers, Trump announced late Friday that he would nominate Esper to replace Mattis on a permanent basis.

“The Department does not discuss meetings with the Commander in Chief — including who is in attendance,” Jonathan Hoffman, a spokesman for the Pentagon, said in a statement. “There is no confusion by anyone at the Pentagon — or to our adversaries — as to who is the head of the United States Department of Defense.”

He said Shanahan would be acting secretary until midnight on Sunday, and Esper will take over the first minute of Monday.

Esper comes with defense qualifications that outstrip Shanahan’s, having served for years as an Army officer, a policy adviser in Congress, a top Pentagon official, a defense industry lobbyist and an executive at a well-known conservative think tank. Most recently, he ran the U.S. Army as its top civilian, overseeing the manning and equipping of the largest branch of the American military by personnel.

Esper studied in the same U.S. Military Academy class as Secretary of State Mike Pompeo, giving him a long-standing relationship with the most important fellow Cabinet official for most secretaries of defense. He also has worked for the past year and a half in tandem with Gen. Mark A. Milley, the top uniformed officer in the Army, who is due to take over this fall from Gen. Joseph F. Dunford Jr. as next chairman of the Joint Chiefs of Staff.

“It’s crucial to have someone at the helm of the Pentagon who can look across the complicated international security landscape, across the regional issues and the functional issues, and recognize the pros and cons of using military force,” said Mara Karlin, a former top Pentagon strategist in the Obama administration who is now a professor at Johns Hopkins University. “Shanahan did not have the political experience or the policy experience to do this, but appeared to be trying.”

Karlin said that Esper has demonstrated a willingness to choose internal winners and losers in his management of the Army — a critical quality for a defense secretary — and also comes with a wealth of other experience in defense matters.

“The question is what does meaningful civilian control of the Pentagon look like?” Karlin said. “I think there is evidence that Army Secretary Esper could exert that. He has worked across the Washington apparatus. He has touched this world from a whole bunch of different perspectives.”

Whether Esper can gain the personal trust of Trump, and feel comfortable expressing independent views in front of the president, remains to be seen. During his nearly six months as acting secretary, Shanahan regularly faced explicit questions about his independence and standing with the president. With the imprimatur of the Senate, Esper may also be able to choose appointees for a number of Pentagon positions occupied by acting officials and build out a more robust staff. 

Esper’s likely confirmation later this year comes after the extraordinary events surrounding Iran, which raised questions for former top officials about the decision-making process involving military action.

Previous presidents, including Obama and Bill Clinton, have made late-stage decisions to stand down on military strikes in the works, but Trump’s description of the moments that led up to his decision is what raised alarm bells for some former officials.

In tweets and an interview with NBC News, Trump said that minutes before the military action was due to launch, he asked his generals how many Iranians would die, and when he heard approximately 150, he stopped the planned strike because he felt it wasn’t proportionate. If the president’s version of events is true, former top Pentagon officials say, it represents at worst a breakdown in the chain of command and at best a departure from the traditional practice of running through the casualty impact of military actions well before any decisions are made.

“I can’t think of a more chaotic situation than to have the president abort an operation while military forces are moving into position to conduct a military action — and do so on the basis that he wasn’t told pertinent information,” said Jeremy Bash, a former top official at the Pentagon and the CIA during the Obama administration. He described that process, if it played out the way Trump described it, as a “train wreck.”

The lack of a confirmed defense secretary during the deliberations Thursday also would have put an unfair onus on the chairman of the Joint Chiefs of Staff, said Eric Edelman, a former U.S. ambassador and top Pentagon official in the George W. Bush administration. The chairman is the official military adviser to the president, but the defense secretary is supposed to present the broader implications of any military options, and they tend to coordinate on their position on a military strike before presenting options to the White House.

“You’ve created this imbalance where you have one guy with a foot out the door and the other guy who hasn’t been nominated yet — how are they going to opine or say anything meaningful that is going to have an impact on the process?” Edelman said. “Then it puts everything in the hands of the chairman, which isn’t fair.”

Ultimately, the decision about the use of force rests with the commander in chief; a deliberative and considered process leading up the decision is designed to give the president confidence that all options were examined carefully. It also can assure the public that decisions possibly resulting in the death of U.S. troops, enemy forces or civilians on the ground are made in a way that isn’t cavalier. 

“The toughest decision a president has to make is to deploy forces in harm’s way. Every president I’ve worked with, that’s what tears their insides out,” Panetta said. “But if you at the very least go through that process — and evaluate all these issues and the consequences — then at the end of the day you have to make a tough decision, but at least it is one that is carefully considered.”