The FBI also was wary of the remote possibility of a “blue on blue” confrontation — between the federal agents searching the location and the Secret Service agents who guard the former president, according to people familiar with the matter, who like others interviewed for this article spoke on the condition of anonymity to describe internal discussions.

“Executing a search like that is sensational enough. Doing it without the former president there is probably the best good-faith effort you can make to reducing the probability of it becoming even more sensationalized,” said Jeffrey Cortese, a former FBI supervisor. “They would want to get in and get out without any complications.”

Leaders of the Justice Department were proceeding cautiously as well, agreeing with the FBI on these points even as tensions sometimes flared between agents and prosecutors.

On the day he became attorney general, Merrick Garland inherited a massive investigation into the pro-Trump riot at the U.S. Capitol on Jan. 6, 2021, which threatened the peaceful transition of power to Joe Biden. Prosecutors were working from the bottom up to see if a criminal case could be made against high-profile people such as Trump over the insurrection or the attempt to sabotage the certification of election results.

The Mar-a-Lago case was very different. There was no ladder for investigators to climb, because the potential target was plainly Trump, suspected of taking highly classified documents when he left the White House and keeping them at Mar-a-Lago, his residence and private club in South Florida, all in apparent violation of the most basic standards of handling national security secrets.

While the Jan. 6 investigation was drawing more headlines, fueled by closely watched prime-time hearings on Capitol Hill, the Justice Department’s decisions about the Mar-a-Lago case put the agency more directly on a collision course with Trump. The nation’s top law enforcement officials knew any misstep could have devastating long-term consequences for the Justice Department, the FBI and the country.

This account of the documents investigation, described by people familiar with the internal workings of the case, shows key and previously unreported moments when authorities decided they had no choice but to take action, and describes the attempts they made to minimize legal risk and avoid mistakes. Their path — from the realization early this year that some classified documents taken to Mar-a-Lago contained nuclear secrets to Garland’s decision last month to appoint a special counsel — illustrates the stark challenges of conducting a criminal probe when the person under investigation is a former president.

Spokespeople for the Justice Department and FBI declined to comment.

Just reaching the decision to seek a court-approved search warrant had presented difficulties. In mid- and late July, lawyers at the Justice Department’s national security division were frustrated with FBI agents at the Washington Field Office, some of whom still weren’t certain there was enough legal justification to conduct a search, people familiar with the situation said. To those lawyers, the doubts expressed by some agents marked another instance in which FBI officials seemed skeptical or gun-shy about investigating Trump in the documents case.

Trump and the Mar-a-Lago documents: A timeline

Inside the top echelons of both the Justice Department and FBI, these people said, everyone understood that a search of Trump’s home would be a fateful step — an acknowledgment that the department, which still bore the political scars of past Trump cases, was conducting its most intrusive investigation yet of the real estate developer turned politician.

Garland, who had vowed to keep partisan politics out of Justice Department decisions, kept close tabs through his senior deputies on what the FBI was doing. Conscious of painful rifts between Justice Department leadership and the FBI during the Trump and Obama eras, he hoped to ensure there was no daylight between the investigators and the prosecutors on this case — and that prosecutors, not investigators, were the ultimate decision-makers.

But given Trump’s many prior battles with the Justice Department and the FBI over investigations into links between Russian officials and members of his 2016 campaign, his transition team and his administration; and possible obstruction of those investigations, officials had little doubt they would come under sustained public attack from Trump and his supporters if they moved forward, people familiar with the situation said.

Letters from Kim Jong Un — and a nuclear discovery

The investigation was born out of a disagreement between Trump and the National Archives and Records Administration, an agency tasked with maintaining the paper trail of presidential history. Under the Presidential Records Act, Archives employees collect and preserve as government property any records created or received as part of the presidency.

In May 2021, with Trump a few months out of office, Archives officials grew worried that some of those records — which legally belong to the public — appeared to be missing. Items widely reported about in the news, such as correspondence from North Korean leader Kim Jong Un were nowhere to be found when archivists looked through their cache of Trump documents.

Agency officials pressed for Trump to return any presidential records. His lawyers alternated between promising cooperation and pleading for more time. The back-and-forth pattern continued for months. To his advisers, Trump downplayed any suggestion there was important or sensitive material in the boxes taken to Mar-a-Lago, according to people familiar with the conversations, insisting that they mostly contained things like newspaper clippings and old golf shirts.

Trump lawyer Alex Cannon notified the Archives by late December that Trump’s legal team had identified a dozen boxes of material, including a letter from President Barack Obama and letters from the North Korean leader, that would be returned to the government. Upon opening what turned out to be 15 boxes, archivists immediately spotted highly classified papers.

FBI officials were skeptical when Archives officials called them on Feb. 7, 2022 — reluctant to get pulled into a dispute about historical records or become an enforcement arm for the Presidential Records Act, people familiar with the discussions said.

15 boxes: The long, strange trip of the boxes sent to the archives from Mar-a-Lago

Agents questioned why it mattered who had which pieces of paper, since presumably any White House documents existed in multiple copies, and probably on computers. Archives officials stressed that while backup copies were helpful, the original documents, including handwritten notes, were essential to following the law on preserving presidential records.

It took several days of phone calls, but gradually the FBI officials came to see one particular set of documents, the Kim letters, as persuasive evidence of a problem; there are obvious national security implications if direct communications from foreign leaders are lost or wrongly circulated.

Agents were also convinced that it mattered if there were sensitive government documents in the boxes, including what one person described as information classified under the Atomic Energy Act, which covers secrets related to nuclear weapons. Some of the paperwork in the boxes was designated as formerly restricted data — a clunky bureaucratic term that also describes secrets related to nuclear matters. Even though the label contains the word “formerly,” such information is still classified.

The FBI knew “as early as the end of February that there were documents at the secret level that were designated as formerly restricted data,” one person familiar with the matter said.

That was a key distinction. Trump has claimed he could declassify things at will — “even by thinking about it. … There doesn’t have to be a process, as I understand it.” Many national security lawyers have publicly disputed that claim. But while a president does have the power to carry out a declassification process for certain documents, the situation is different for material covered by the AEA. Declassifying such documents requires formal approval from other parts of the government.

A slow move into high gear

For the FBI to look at the material the Archives was describing required approval from President Biden’s White House counsel, according to the Presidential Records Act. That took until April, and it wasn’t the only procedural hurdle. Archives officials also had to notify Trump of their intention to let agents go through the classified documents.

Law enforcement officials initially saw little point to launching an investigation in which, even before the case was opened, the potential target of the probe would be notified. Once that did happen, Trump’s lawyers argued for more time and were able to put off the FBI review for a number of weeks, to the frustration of both the Archives and the Justice Department.

Trump lawyers tried to pump the brakes on the investigation by asserting executive privilege, but government lawyers concluded a former president cannot try to invoke the privilege against a sitting president; case law, they noted, largely supports the idea that executive privilege lies with the current occupant of the White House.

In mid-May, FBI agents finally reviewed the boxes sent to the Archives and confirmed the agency’s findings: They contained 184 classified documents — more than 700 total pages worth of secrets.

So the FBI dove in, if only to control a leak or “spillage” of classified material and get the sensitive papers back under government lock and key. To that end, prosecutors secured a grand jury subpoena to Trump’s office demanding the return of all manner of classified documents, including a category for any secrets about nuclear weapons.

Agents discreetly interviewed Trump employees, and those conversations only raised more alarms that the former president was, incredibly, still trying to hold onto classified documents and mislead the government.

The rules of the classification system are complex and rigid, meant to keep a small army of those with high-level security clearances from hoarding, losing or, worst of all, sharing national security information. But the enforcers of those laws had never contemplated the scenario they now faced: a former president allegedly stashing hundreds of documents in a place without the necessary protections.

Trump’s secrets: How a records dispute led to the FBI search of Mar-a-Lago

When intelligence officers, military officials or special agents get security clearances, they have to sign documents swearing they will follow classification rules and not mishandle sensitive material. Prosecutors often use those signed statements when they charge people with mishandling classified information. But presidents do not go through that same paperwork process.

The grand jury subpoena, however, served as a different kind of bright legal line to Trump. Fail to comply, and the consequences could be criminal charges.

In early June, Jay Bratt, a senior Justice Department official, led a small group of law enforcement officials to Mar-a-Lago to underscore the seriousness of the issue.

To investigators, the vast property presented security concerns beyond the storage of highly classified information in a private home rather than a secure government facility. As a private club, it welcomes not just members but also their guests, often with little or no vetting. The estate is a popular venue for weddings and political fundraisers, with Trump often on hand to welcome guests and eat — including his infamous dinner last month with antisemitic rapper Ye, formerly known as Kanye West, and white supremacist and antisemite Nick Fuentes.

How Donald Trump jettisoned restraints at Mar-a-Lago after leaving the White House

Bratt’s team was handed a tightly taped envelope that contained 38 classified documents and a sworn statement signed by Christina Bobb, a lawyer who had only very recently taken on the role of custodian of records for Trump’s office. The statement insisted that a “diligent search” had been conducted for any material with classified markings.

But there were signs that Trump’s team might be concealing something. When Bratt’s team visited the basement storage room where many of Trump’s White House boxes were kept, they were not allowed to open the containers and look inside, according to court papers.

Separately, the Justice Department and FBI were discovering incriminating evidence that Trump or those around him might be actively trying to hide and hold onto additional classified documents.

Agents had interviewed Walt Nauta, a former White House valet who followed Trump to Florida to continue working for him. Nauta told the agents when first approached that he knew nothing about classified documents, or the boxes that contained them. But the more people the FBI spoke to, the more they doubted that claim. When agents interviewed Nauta a second time, he told a much different story: that he’d moved boxes from the storage room to Trump’s residence, after the subpoena was served, and that he’d done so at Trump’s request, according to people familiar with the matter.

With Nauta’s account, the investigation that had sputtered to life months earlier started barreling forward, gathering evidence and momentum, according to people familiar with the case.

For a significant stretch of mid-2022, Garland received almost daily updates on the investigation’s progress, these people said. He relied on staffers with experience as Supreme Court law clerks and litigators to scrutinize legal papers for any potential vulnerability. Early in his tenure as attorney general, Garland’s trademark attention to detail struck some Justice Department officials as unnecessary micromanaging. But when it came to Mar-a-Lago, people familiar with the situation said, that degree of care seemed like an advantage.

During the Obama administration, Garland had been considered to succeed Robert S. Mueller III as FBI director, a position ultimately filled by James B. Comey in 2013. Three years later, Comey would play an outsize role in the presidential contest between Democrat Hillary Clinton and Republican Trump, announcing just days before voters headed to the polls that Clinton — for the second time in a little over a year — was under investigation.

In doing so, Comey broke with law enforcement traditions surrounding investigations and elections, and was harshly criticized. The 2016 investigations of Clinton and Trump were marred by the FBI’s distrust of Justice Department leaders, and reflected a growing distance between the two key arms of federal law enforcement.

Garland, a longtime appeals court judge and former federal prosecutor known for his low-key demeanor, took a very different approach.

As spring turned to summer, and the Justice Department concluded that Trump probably had not turned over all the secret documents he possessed, prosecutors began to contemplate adding to the list of potential charges against Trump: obstruction of justice, if he deliberately flouted the subpoena; and destruction of government documents, if that’s what he’d done rather than return them.

That meant considering whether to get a search warrant for the former president’s home and office — an unprecedented action that was sure to enrage Trump, his supporters, and his most ardent backers in Congress, and risked tarnishing the Justice Department’s reputation in exactly the way Garland had feared.

Over many weeks of discussions, senior FBI officials made clear that they would only do a search if it was authorized by the attorney general himself. If the Justice Department and FBI were going to take the giant leap of sending agents into Trump’s home to seize documents, they were going to make that leap together, hand in hand. Senior Justice Department officials agreed, according to people familiar with the conversations.

But there were, these people said, tensions at that time between the Justice Department’s national security prosecution team, which was led by Matthew Olsen, and some agents at the FBI’s Washington Field Office, which was led at the time by Steven D’Antuono. The lawyers, these people said, felt they had amassed more than enough probable cause to ask a judge to approve a search of Mar-a-Lago. Some agents at the field office weren’t certain. Eventually, the Justice Department lawyers prevailed.

Around that time, some law enforcement officials still held out hope that they would not have to conduct a search if Trump’s legal team changed course and was more forthcoming. Prosecutors were also still working to get security footage from Mar-a-Lago — footage that would ultimately confirm some of what Nauta, the Trump aide, had said about moving boxes.

The status of key investigations involving Donald Trump

“We had been talking for a long time, asking for a long time. At some point, you’re not asking anymore,” one person familiar with the investigation said about the decision to seek the warrant.

The concerns about Trump not being at Mar-a-Lago on the day of the search seemed to be a relatively easy problem to solve, since during the hot summer months, he rarely stayed there.

On Friday, Aug. 5, FBI agents got approval from a federal magistrate judge in Florida to conduct a search.

Three days later, deliberately dressed down in khakis and polo shirts to try to lower their profile, agents showed up at Mar-a-Lago with the warrant. They spent hours combing Trump’s storage room, residence and office, finding 103 classified documents — some in Trump’s desk, according to court papers. They also took about 13,000 nonclassified documents as part of the investigation.

Combined with the documents previously recovered from the boxes sent to the Archives and the envelope turned over in June, the former president had kept at least 325 classified items at his private club and resort. Sixty were marked top secret, according to court papers. Some included highly classified information about a foreign country’s nuclear capabilities, Iran’s missile program and U.S. intelligence-gathering aimed at China, according to people familiar with their contents.

Trump denounced the “raid” as a violation of his rights, and political targeting of a likely presidential candidate. As the news of the operation consumed public attention, Trump escalated his attacks on the investigators, suggesting — without any supporting information — that the FBI had planted evidence, and that as president he had declassified “everything” found by agents. National security experts noted that declassified documents usually have additional markings indicating they are no longer secret.

Three days after the search — amid a marked increase in threatening statements about federal law enforcement across the country, much of it in response to the Mar-a-Lago operation — a gunman tried to attack the FBI office in Cincinnati. The 42-year-old Navy veteran, who had previously been on the FBI’s radar as a possible far-right extremist, was fatally shot by police after a chase led to a six-hour roadside standoff.

Garland took the unusual step of summoning news cameras to Justice Department headquarters that day to explain that he personally approved the decision to search Mar-a-Lago. He also defended the FBI and Justice Department officials.

“The men and women of the FBI and the Justice Department are dedicated, patriotic public servants,” he said. “Every day they protect the American people from violent crime, terrorism and other threats to their safety while safeguarding our civil rights. They do so at great personal sacrifice and risk to themselves.”

In the aftermath of the search, Trump’s lawyers fought to have an outside legal expert, known as a special master, review the documents taken by FBI agents to see if any should be withheld from investigators. That demand, initially granted by a federal judge in Florida before an appeals court overruled her, delayed some elements of the investigation.

A review of the seized classified documents did not reveal an apparent financial motive for taking them. As best as investigators were able to determine in the months following the search, Trump’s motive in refusing to return the material seemed to be primarily ego, and petulance, according to people familiar with the matter.

In mid-November, at Mar-a-Lago, Trump formally announced he would run for president in 2024. Within days, Garland took a step he had hoped to avoid, people familiar with his thinking said. He named a special counsel within the Justice Department to oversee the classified-documents investigation and the investigation of events leading up to Jan. 6, a probe that had expanded to examine the conduct of Trump and those in his immediate circle.

Jan. 6 House panel asks Justice Dept. to charge Trump with four criminal counts

The Justice Department’s special counsel regulation was originally designed to give the public confidence that prosecutors could fairly investigate a case even when there is a political conflict of interest for leaders of the agency. By 2022, however, many senior law enforcement officials had privately expressed doubts that the role carries much credibility with the American public anymore.

Two special counsels were appointed during the Trump administration — one who investigated connections between Russia and the Trump campaign, as well as the president’s own conduct, and another to investigate the people who investigated those things. In the beginning, each appointment was hailed by partisans as a political death knell for high-profile figures. But both disappointed their biggest fans when they failed to topple those targets.

With Trump running, and Biden saying he would likely seek reelection, Garland said he had little choice but to appoint a special counsel, citing “extraordinary circumstances” and the need to maintain public trust. He chose Jack Smith, a longtime federal prosecutor who once headed the Justice Department’s public integrity section and has spent recent years as a Kosovo war crimes prosecutor at The Hague.

A special counsel still answers to the attorney general, but has a greater degree of autonomy than other Justice Department prosecutors.

Officials pledged that the appointment would not slow down the investigations, even as Smith spent another month in the Netherlands recovering from a knee injury.