The investigation reaches back to the end of Trump’s term.

At the end of President Donald J. Trump’s term in January 2021, a trove of documents — many which were said to be in the White House residence — were packed in boxes along with clothes, gifts, photos and other material, and shipped by the General Services Administration to Mar-a-Lago, his home and resort in Florida.

By May of that year, the National Archives and Records Administration alerted Mr. Trump’s lawyers that the agency was aware that he had taken with him boxes that could contain government records, setting off a months long back-and-forth between the agency and Mr. Trump.

That December, Mr. Trump’s lawyers told the National Archives that they had boxes of material that could be reclaimed, and the agency arranged for the boxes — which ultimately totaled 15 — to be retrieved.

When archivists opened the boxes, they discovered that 14 of them contained documents marked as classified. The National Archives alerted the Justice Department and an investigation was opened into whether the materials had been mishandled.

Around that time, Mr. Trump told an aide on multiple occasions to tell archives officials that he had given everything back — which later proved not to be true.

In the months that followed, the Justice Department tried to ensure that it had obtained any other documents that may have ended up at Mar-a-Lago. In May 2022, the Justice Department issued a subpoena to Mr. Trump’s lawyers for any additional records still in his possession.

That June, Justice Department and F.B.I. investigators went to Mar-a-Lago, where Mr. Trump’s lawyers gave them roughly three dozen additional documents that had been found in a storage room, including 17 bearing the “Top Secret” label.

In an apparent effort to show the Justice Department that all the material in question had been returned, one of Mr. Trump’s lawyers signed an attestation on June 3, 2022, stating that a “diligent search” had turned up no other documents.

The Justice Department subsequently sent Mr. Trump’s lawyer a letter asking that the room where the boxes were being held be secured and the materials be secured.

The Justice Department developed additional evidence, including from surveillance cameras near the storage room, that gave them probable cause that documents had been withheld.

After getting a search warrant, the F.B.I. descended on Mar-a-Lago on Aug. 8, 2022. Agents combed through Mr. Trump’s property, finding more than 100 additional classified documents that were discovered in the storage room and Mr. Trump’s office.

“That the F.B.I., in a matter of hours, recovered twice as many documents with classification markings as the ‘diligent search’ that the former president’s counsel and other representatives had weeks to perform calls into serious question the representations made in the June 3 certification and casts doubt on the extent of cooperation in this matter,” the Justice Department wrote in a court filing two weeks after the search.

Mr. Trump — who announced the search to the world several hours after it occurred — quickly clashed with investigators. He tried to fight the Justice Department to have the materials set aside and a special master appointed to look over investigators’ shoulders. Mr. Trump won an early court victory in that matter, but ultimately lost and the department proceeded with its investigation.

In the months that followed, a range of Trump aides and lawyers were interviewed by the F.B.I. and Justice Department prosecutors. Some of them tried to have federal judges block the Justice Department from questioning them, but those efforts largely failed as well.