The Justice Department kept open the investigation into Hillary Clinton’s family foundation for nearly all of President Donald J. Trump’s administration, with prosecutors closing the case without charges just days before he left office.
Newly released documents and interviews with former department officials show that the investigation stretched long past when F.B.I. agents and prosecutors knew it was a dead end. The conclusion of the case, which centered on the Clinton Foundation’s dealings with foreign donors when Mrs. Clinton served as secretary of state under President Barack Obama, has not previously been reported.
Mr. Trump, who campaigned on a promise to “lock her up,” spent much of his four-year term pressuring the F.B.I. and the Justice Department to target political rivals. After being accused by the president’s allies of serving as part of a deep-state cabal working against him, F.B.I. officials insisted that the department acknowledge in writing that there was no case to bring.
The closing documents, which were obtained by The New York Times as part of a Freedom of Information Act lawsuit, spelled the end to an investigation that top prosecutors had expressed doubts about from the beginning. Still, it became a rallying cry for Republicans who believed the F.B.I. would ultimately turn up evidence of corruption and damage Mrs. Clinton’s political fortunes.
The foundation became attack fodder for Republicans in 2015 after the conservative author Peter Schweizer published the book “Clinton Cash: The Untold Story of How and Why Foreign Governments and Businesses Helped Make Bill and Hillary Rich,” an investigation of donations that foreign entities made to the family organization. Mr. Schweizer is the president of the Government Accountability Institute, where Stephen K. Bannon, Mr. Trump’s former chief strategist, was a founder and the executive chairman.
A spokesman for the Clinton Foundation, Craig Minassian, said that the organization had been “subjected to politically motivated allegations with no basis in fact.”
Republicans seized on the accusations in Mr. Schweizer’s book, accusing Mrs. Clinton of supporting the interests of foundation donors as part of a quid pro quo.
Specifically, critics focused on the foundation’s receipt of large donations in exchange for supporting the sale of Uranium One, a Canadian company with ties to mining stakes in the United States, to a Russian nuclear agency. The deal was approved in 2010 by the Committee on Foreign Investment in the United States when Mrs. Clinton, as secretary of state, had a voting seat on the panel.
Mr. Schweizer’s research caught the eye of F.B.I. agents in Washington, who in 2016 opened an investigation into the allegations in his book.
The F.B.I. in New York and Little Rock, Ark., also opened investigations but apparently not based on the book, according to the final report by John H. Durham, the Trump-era special counsel who led an investigation into the bureau’s inquiry into possible ties between Mr. Trump’s campaign and Russia.
In his report, which was made public last week, Mr. Durham explored the handling of the Clinton Foundation investigation, comparing it to the F.B.I.’s treatment of the Russia investigation. As part of his inquiry, Mr. Durham questioned Mrs. Clinton last spring. “Secretary Clinton was voluntarily interviewed by Special Counsel Durham on May 11, 2022,” said David E. Kendall, her lawyer. “No topics were off limits. She answered every question.”
The Justice Department did not think much of the foundation investigations, frustrating F.B.I. agents. Raymond N. Hulser, a prosecutor in charge of the public integrity section at the time, told Mr. Durham that the Washington case that was based on the book lacked predication.
Indeed, some prosecutors at the time believed the book had been discredited.
The investigation became a source of friction at the F.B.I. as agents believed the Justice Department had stymied their work.
That tension spilled into public view and had far-reaching consequences.
Andrew G. McCabe, then the F.B.I.’s deputy director, was accused of leaking information about the case to a Wall Street Journal reporter and later lying about it to the Justice Department’s inspector general. The episode helped prompt his dismissal in 2018 and a failed effort by the department to prosecute him.
In August 2016, the three foundation cases were consolidated under the supervision of agents in New York. Agents were authorized to seek subpoenas from the U.S. attorneys’ offices in Manhattan and Brooklyn, but prosecutors declined to issue them. The investigation seemed to go dormant.
Ultimately, the F.B.I. moved the case to Little Rock. In 2017, after prosecutors there requested help, the deputy attorney general’s office said the Justice Department would support the case.
Eventually, prosecutors secured a subpoena for the charity in early 2018 and the F.B.I. detailed personnel to examine donor records. Investigators also interviewed the former chief financial officer for the foundation.
Career prosecutors in Little Rock then closed the case, notifying the F.B.I.’s office there in two letters in January 2021. But in a toxic atmosphere in which Mr. Trump had long accused the F.B.I. of bias, the top agent in Little Rock wanted it known that career prosecutors, not F.B.I. officials, were behind the decision.
In August 2021, the F.B.I. received what is known as a declination memo from prosecutors and as a result considered the matter closed.
“All of the evidence obtained during the course of this investigation has been returned or otherwise destroyed,” according to the F.B.I.
Jo Becker contributed reporting.