WASHINGTON — The Justice Department’s search of former President Donald J. Trump’s Florida home was spurred by the discovery that he had retained a trove of highly classified material that included documents related to the use of “clandestine human sources” in intelligence gathering, according to a redacted version of the affidavit used to obtain the search warrant.
The portions of the affidavit made public on Friday describe the Justice Department’s monthslong push to recover sensitive materials taken from the White House by a former president who viewed state documents as his private property, and now faces a department investigating the possibility he illegally obstructed those efforts.
The partial release of the 38-page affidavit was the latest in a remarkable succession of developments in the inquiry into how hundreds of pages of documents with classified markings ended up at Mr. Trump’s Mar-a-Lago residence after he left the White House, in apparent violation of the law requiring all presidential materials to be turned over to the National Archives.
The filing also documents in exhaustive detail efforts by the archives and Justice Department to claw back the material in Mr. Trump’s possession without resorting to a search that would, inevitably, create a powerful political backlash from the former president and his supporters.
The heavily redacted affidavit was unsealed more than two weeks after F.B.I. agents descended on Mr. Trump’s Mar-a-Lago residence and private club with a court-authorized search warrant, carting off additional material marked as classified, citing possible violations of the Espionage Act and obstruction of justice statutes.
There was “probable cause to believe that evidence of obstruction will be found” at Mr. Trump’s house, prosecutors wrote in the affidavit requesting the search. The redacted document did not offer details of what the possible obstruction might be, but the mention raised the possibility that the former president could face considerable legal peril.
Highlighting concern among officials that Mr. Trump or his followers could seek to interfere with the investigation, the Justice Department said it had requested extensive redactions of the affidavit in part to protect “a significant number of civilian witnesses” with knowledge of Mr. Trump’s actions.
The affidavit, which was sworn to on Aug. 5, also noted that the F.B.I. had “not yet identified all potential criminal confederates nor located all evidence related to its investigation.”
Under orders from the judge in the case, Bruce E. Reinhart, the Justice Department had proposed extensive redactions to the affidavit in an effort to shield witnesses from intimidation or retribution. The government did so to protect the broader integrity of its inquiry into whether Mr. Trump had violated the law by willfully retaining national security records.
Though the government redacted details pertaining to witnesses in the Mar-a-Lago investigation, the affidavit vividly describes the dangers posed if their identities, or even actions, were made public.
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Witnesses, two department lawyers wrote, could be subjected to “retaliation, intimidation or harassment, and even threats to their physical safety” — adding that Judge Reinhart himself had already noted those dangers were “not hypothetical in this case.”
The search, the affidavit reveals, was prompted by an intensive F.B.I. review of an initial 15 boxes of materials that Mr. Trump turned over to the archives in January, after months of government pressure.
In those boxes, they found a total of 184 documents with classification markings, including 25 labeled “top secret.” Others were marked in a way suggesting they were related to foreign intercepts collected under the Foreign Intelligence Surveillance Act.
Some of the documents, the affidavit said, were from the Sensitive Compartmented Information programs, a designation that is one of the most tightly restricted categories of secrecy. Still others had been labeled “originator controlled,” meaning they could not be held without the approval of the intelligence community. Several of the documents, the affidavit said, contained what appeared to be Mr. Trump’s handwritten notes.
But agents were most alarmed to discover that many of the materials included the highest national security restrictions, requiring they be held in controlled government storage facilities, and barring them from ever being shared with foreign governments, to protect “clandestine human sources,” or informants employed by the intelligence community to collect information around the world.
The affidavit does not disclose the nature of the material or why Mr. Trump chose to retain it.
Hours after the affidavit was released, Mr. Trump’s lawyers submitted a clarification to a motion they had filed on Monday asking a different federal judge in Florida to appoint an independent arbiter called a special master to weed out any documents seized in the search that were protected by executive privilege. After receiving the confusing initial filing, the judge in the case, Aileen M. Cannon, had asked the lawyers to answer some basic legal questions, including why she had jurisdiction over the matter and what exactly they were asking her to do.
In their new filing, the lawyers said that only a full district judge like Judge Cannon could order a special master, not a magistrate judge like Judge Reinhart. They also said the released affidavit provided “almost no information that would allow” Mr. Trump “to understand why the raid took place, or what was taken from his home” and requested a detailed inventory of the items seized by the F.B.I.
Among the documents unsealed by the Justice Department was a May 25, 2022, letter from one of Mr. Trump’s lawyers, M. Evan Corcoran, to Jay Bratt, the chief of the Justice Department’s counterintelligence and export control section, who is leading the investigation into Mr. Trump’s handling of sensitive documents.
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In the letter, Mr. Corcoran tried to play down the dispute about the documents. He claimed that Mr. Trump’s dealings with the archives had been “a voluntary and open process” and argued that the president has absolute authority to declassify documents. Department officials appended the letter to offer Mr. Trump’s team an opportunity to defend his actions.
But notably missing was an assertion that Mr. Trump and his allies started pushing after the search at Mar-a-Lago: that Mr. Trump had issued a standing order to declassify anything he took out of the White House.
It was the government’s frustration with the negotiations, along with security concerns and the continued unwillingness of Mr. Trump to return sensitive documents that remained in his possession, that prompted the department’s leaders to move as quickly as they did, according to officials.
The question of obstruction was front and center when the partly redacted affidavit was made public on Friday. A statute related to obstruction was among those used to underpin the case for a warrant. Questions have emerged about whether Mr. Trump or his team were obstructing the investigation into additional documents.
The redactions, which conceal roughly half of the affidavit’s text in black bars, covered many of the most sensitive details of the Justice Department’s investigation. Whole swaths of the filing are redacted, including most of pages 11 through 16. As a result, there are limited references to the witnesses or investigative methods that led to the findings laid out by lawyers with the department’s national security division, who persuaded Attorney General Merrick B. Garland to sign off on the highly unusual request for a search.
On Friday morning, before the documents were released, Mr. Trump attacked the department on Truth Social, the social media platform he uses to communicate since being banned from Twitter after the Capitol attack on Jan. 6, 2021. He called the Justice Department and the F.B.I. “political Hacks and Thugs” who “had no right under the Presidential Records Act to storm Mar-a-Lago and steal everything in sight, including Passports and privileged documents.”
He spent much of this week huddling with his lawyers to discuss the array of legal problems he now faces, according to a person with knowledge of the situation.
Shortly after the release of the affidavit, Karine Jean-Pierre, the White House press secretary, told reporters it was “not appropriate for us to comment on this.”
That the affidavit was made public was, in itself, an extraordinary step. Such documents are almost always left entirely sealed until criminal charges are filed, and even then, they tend to emerge only as important legal issues in a case are litigated. There is no indication the Justice Department plans to file charges in the documents case anytime soon.
The partial release came after several news organizations, including The New York Times, filed a motion this month asking Judge Reinhart to unseal the entire document, citing enormous public interest in the search of Mar-a-Lago.
The Justice Department responded by saying that doing so would provide a road map to its investigation and wanted Judge Reinhart to keep the affidavit fully under wraps. Mr. Trump’s lawyers did not object, to the astonishment of Mr. Garland’s team, who believe the disclosures portray the former president’s actions in a deeply unflattering light.
At a hearing last week, Judge Reinhart, apparently seeking a middle ground, floated the idea of releasing portions of the affidavit. He ordered the government to send proposed redactions to him by Thursday at noon and issued his decision to release the redacted version within hours.
Justice Department officials had suggested they would push hard to scrub anything that could expose witnesses in the case. After the search at Mar-a-Lago, the F.B.I. reported a surge in threats against its agents; an armed man tried to breach the bureau’s Cincinnati field office before being killed in a shootout with the local police.
The Trump team has sought to portray the search as unjust and unnecessary, claiming there were continuing talks between Mr. Trump’s side and the Justice Department that led to the first tranche of boxes of documents being returned to the archives in January.
Prosecutors describe the exhausting back-and-forth between Mr. Trump and officials from the archives that consumed much of 2021.
The narrative picks up momentum on Feb. 9, 2022, when the National Archives found that the 15 boxes of material contained highly classified records that were “unfoldered,” misidentified or mixed up with other records. They discovered mountains of paper — more than 700 pages of classified documents, some of the most sensitive and restricted that exist in government, known as Special Access Programs.
In early May, as Mr. Trump’s lawyer unsuccessfully argued the material was protected by executive privilege, the F.B.I. examined the contents and identified threats to the intelligence community.
As early as last summer, Mr. Trump repeatedly resisted entreaties from several advisers to turn over the material, according to multiple people briefed on the matter. “They’re mine,” he said of the boxes, according to three people familiar with what took place.
The former president went through at least some of the boxes in late 2021, although it is unclear if he went through them all. In their letter, Mr. Trump’s lawyers described the documents with classified markings as packed “unknowingly” and sent to Mar-a-Lago.
By June, the conflict was coming to a head. His lead lawyers in the case met on June 3 with Mr. Bratt, the chief of the counterespionage section of the national security division at the Justice Department. Shortly before that meeting, Mr. Corcoran, Mr. Trump’s lawyer, went to the basement to search through the boxes for classified material, according to two people briefed on the matter.
The released affidavit does not reveal the amount of classified material turned over to federal officials as the result of that June 3 meeting, which came after the grand jury had been formed.
But it is clear those actions did not satisfy the government. By this time, the Justice Department had gathered information from at least one witness suggesting that there might be more presidential material at Mar-a-Lago. On June 22, the department subpoenaed surveillance footage from various places in the club, including the hallway outside a basement storage area that Mr. Bratt had toured nearly three weeks earlier to see where documents had been kept.
The video showed boxes being moved out of the storage room sometime around the contact from the Justice Department, people familiar with the tapes said. And it also showed boxes being slipped into different containers, which alarmed investigators.
As the temperature rose, so did the heat on the former president.
On Aug. 8, investigators found additional material, presidential records and classified documents in the basement area, as well as in a container on the floor of Mr. Trump’s closet in his office, a former dressing room in the bridal suite above the club’s ballroom.
The closet had a hotel-style safe, but it did not contain the materials investigators sought and was too small to hold the documents he had, according to several people familiar with the events.
Neil Reisner contributed reporting.