WASHINGTON — Questions raised by the F.B.I. about the State Department’s handling of Hillary Clinton’s emails have cast a cloud of doubt over the political futures of a number of her top advisers, including some expected to hold high-level jobs in her administration if she is elected president.
Though Attorney General Loretta E. Lynch formally affirmed on Wednesday that the Justice Department would not seek criminal charges against anyone in the email case, fallout from the matter is sure to affect several dozen State Department advisers who, records show, facilitated Mrs. Clinton’s unorthodox email arrangement or used it to send her classified documents.
Among those drawing the most intense scrutiny are Cheryl Mills, Huma Abedin and Jake Sullivan, onetime aides who could face difficult questions in pursuing security clearances for diplomatic or national security posts because of their involvement with Mrs. Clinton’s emails.
The State Department said it would restart an internal review into the handling of Mrs. Clinton’s emails now that Justice’s investigation is formally closed, and that review could threaten the security clearances of several dozen other career officials and political appointees who knew of Mrs. Clinton’s private email server.
As for Mrs. Clinton, House Speaker Paul D. Ryan said Wednesday that in light of the F.B.I.’s findings, intelligence officials should deny her the classified briefings normally given the major nominees.
“I’ve never seen anything quite like this,” Bill Savarino, a Washington lawyer specializing in security clearances, said on Wednesday. “You’ve got a situation here where the woman who would be in charge of setting national security policy as president has been deemed by the F.B.I. unsuitable to safeguard and handle classified information.”
In a briefing Tuesday on the F.B.I.’s findings, the agency’s director, James B. Comey Jr., said that in situations similar to Mrs. Clinton’s, people found to have mishandled classified information “are often subject to security or administrative sanctions.”
He also criticized what he said were inadequate security measures at the State Department in the handling of classified material, a characterization the department has strongly disputed.
While Mr. Comey’s criticism of Mrs. Clinton attracted the most attention on Tuesday, his comments included other unnamed colleagues.
“Although we did not find clear evidence that Secretary Clinton or her colleagues intended to violate laws governing the handling of the classified information,” Mr. Comey said, “there is evidence that they were extremely careless in their handling of very sensitive, highly classified information.”Indeed, a review of thousands of pages of emails and depositions that have been made public over the last two months shows that State Department officials ignored numerous red flags about the problems created by Mrs. Clinton’s use of a private server, both in the handling of classified information and the preservation of public records.
Those few employees who raised questions about the email arrangement were told to keep quiet about it, the State Department inspector general found.
Mrs. Clinton herself seemed glib at times about the risks posed by her private email system. In one email exchange in 2011, she was puzzled about how emails from her private account to a State Department employee ended up in the aide’s Gmail account, and jokingly blamed foreign hackers. “Maybe the Chinese hacked it and focused on you!” she wrote.
A federal court ordered a number of State Department aides to give lengthy depositions about their knowledge of Mrs. Clinton’s email system as part of a lawsuit brought by Judicial Watch, a conservative advocacy group.
Her top aides said they gave little thought to the problems that the private server might create. Both Ms. Mills and Ms. Abedin said they now regretted the lack of attention they had given to the system, while other officials said they simply did not remember much about how it was set up and used.
In a deposition last week, Patrick F. Kennedy, the under secretary of state for management and operations, said repeatedly that he could not recall details about Mrs. Clinton’s email use, even though he responded to emails from her.
Asked if her use of a personal email address raised any questions in his mind, he said that “it did not strike any bells in my mind, no.”
“Why not?” the lawyer for Judicial Watch asked.
“Because it did not,” Mr. Kennedy said.
The State Department has continued to defend its handling of classified material, and it challenged Mr. Comey’s assertions about a small number of the Clinton emails that were marked as classified.
John Kirby, the department’s spokesman, said Wednesday that because of “human error,” one of Mrs. Clinton’s aides at the time, Monica R. Hanley, had mistakenly marked as classified two emails involving routine diplomatic phone calls to foreign leaders. Those appeared to be ones that Mr. Comey singled out as bearing classified markings, in this case designating them as “confidential,” but Mr. Kirby said that information that was initially considered classified was not by the time Mrs. Clinton decided to make the calls.
It was not clear if Mr. Comey also referred to other emails with such markings.
Sean M. Bigley, a Los Angeles lawyer who specializes in security clearances, said the handling of classified information could be “a major issue” for officials who sent emails that ended up on Mrs. Clinton’s server. He said his firm has routinely defended clients who have lost their security clearances — often a requirement for employment — because of violations “much less egregious” than what Mr. Comey described.
“The folks who were involved with this, even on a peripheral basis, at least are going to be facing administrative action, or should be, based on the historical cases we’ve dealt with,” he said.
Mr. Savarino, the Washington lawyer, shared that assessment. He said that if any of Mrs. Clinton’s former aides involved in the email controversy were to approach him for help in seeking a future clearance, “I’d tell them that ‘you’ve got a fight on your hands.’”
Decisions on security clearances rest with the hiring agencies. At the White House, the Executive Office of the President makes these decisions based on background checks conducted or overseen by the F.B.I., sometimes with the help of outside contractors. But even if a clearance is rejected, the president has the power to overturn that decision and order the clearance.
The rules for security clearances — including challenging decisions to strip them — were signed by President Clinton in 1995 in the wake of the Aldrich Ames spy scandal.
Mr. Bigley said that contrary to Mr. Comey’s characterization, the State Department practiced strict enforcement on matters that could affect security clearances, which include not only the mishandling of classified information, but also financial problems, exposure to foreign influences, drug and alcohol abuse and other personal misconduct that could expose an official to blackmail by a foreign intelligence agency.
He said the threshold for administrative punishment — including suspension of a clearance — was much lower than for criminal prosecution. Without disclosing specific clients, he cited cases involving government employees penalized for bringing their cellphones into secured areas or making Skype calls from a specially designated room, known as a SCIF: Sensitive Compartmented Information Facility.
“Ten, 20-year careers we’ve had completely ruined because of mistakes like that,” he said.
Cases are routine, but often shrouded in secrecy. Only two agencies — the Pentagon and the Department of Energy — publish records of decisions. The Pentagon’s, which covers private military contractors, showed that 1,657 cases were adjudicated in 2015.
In a letter in May to the State Department, Senator Charles E. Grassley, the Iowa Republican who leads the Senate Judiciary Committee, tried to find out whether a number of former Clinton aides, including Ms. Abedin, Mr. Sullivan and Philippe Reines, have kept their security clearances, “in light of the fact that classified information has been discovered” on Mrs. Clinton’s private server.
The State Department declined to tell him, saying it would not discuss the status of individuals’ security clearance.
Mr. Grassley pushed the issue again Wednesday, asking Mr. Comey in a letter whether the F.B.I. had recommended that Mrs. Clinton or any of her senior aides lose their security clearances.
“If not,” the senator asked, “why not?”
(via: New York Times)