A New F.B.I. Director Prepares to Take the Reins WASHINGTON - James B. Comey will begin shadowing the F.B.I. director, Robert S. Mueller III, next week as he prepares to take on the job himself. Mr. Comey was a deputy attorney general under President George W. Bush but has not had a government job since 2005. So he will have to acquaint himself with the latest threats to the United States - as well as the whereabouts of the men's room at the bureau's headquarters here. But his off-the-job training stops Sept. 5, when Mr. Comey will take over from Mr. Mueller and begin a 10-year term. Under Mr. Mueller, the Federal Bureau of Investigation transformed itself into a counterterrorism agency after the Sept. That is still the bureau's chief priority, but Mr. Comey is likely to spend the next year dealing with the impact of a much different problem: the automatic budget cuts known as sequestration, according to current and former senior F.B.I. officials. In one of his final interviews as director, Mr. Mueller said Wednesday that sequestration had forced the bureau to cut back on plans to expand its cyberterrorism fight, had limited officer training, and had reduced the kind of aid to states and local police forces that helps them solve crimes like kidnappings. And the bureau has told its roughly 35,000 employees to expect to be furloughed for 13 to 15 days starting in October, senior F.B.I. officials said. Difficult decisions about how the F.B.I. should allocate its resources are "going to be the biggest hurdle he faces at this juncture," Mr. Mueller said about Mr. Comey. We had to take monies out of these programs last year to ensure that we could keep people on the street. According to current and former bureau officials who have talked to Mr. Comey, he does not have any grand designs to immediately change the bureau. They said he planned to spend the first few months learning as much as he could and listening to its agents and analysts before making any changes. One of the most politically contentious issues Mr. Comey will face, current and former bureau officials say, is the continuing investigation into the attacks on the United States mission in Benghazi, Libya, on Sept. 11, 2012, that killed Ambassador J. Christopher Stevens. Congressional Republicans have accused the Obama administration of covering up information about the attacks and have said that the F.B.I. has not moved quickly enough to investigate. Agents have grown frustrated with the Libyan government, which has little control over parts of the country where the militants who carried out the attacks are believed to be based, and with the State Department, which has the lead in dealing with the Libyans. The Justice Department has charged at least some of the suspects, but there have still been no arrests. It is not clear when arrests will be made or where any trial would be held. Another issue for Mr. Comey is cybersecurity. For the past several years, Mr. Mueller has said that the United States needs to develop a greater sense of urgency about threats to the country's infrastructure, and he has called on Congress to pass legislation to protect the United States from cyberattacks. Last year, Congressional Republicans thwarted administration efforts to pass sweeping cybersecurity legislation. Mr. Comey could pick up where Mr. Mueller left off, and become a public advocate for cybersecurity legislation. In his final interview, Mr. Mueller said one of his top fears was that terrorists could acquire "a weapon of mass destruction" - even in digital form that could disrupt the power or financial systems. Mr. Mueller reiterated his defense of the National Security Agency's surveillance efforts, insisting that they are legal and an essential part of the country's antiterrorism efforts. Disclosures by Edward J. Snowden, the former security contractor for the agency, have had repercussions around the world, Mr. Mueller said, though he declined to elaborate. Mr. Mueller said little that was revealing. His hair was a significantly lighter shade of gray than in the portrait that hangs behind the security desk at the F.B.I. headquarters in Washington, where he spoke to reporters over cookies and ice water as part of a last round of public comments before he steps down on Sept. He said in addition to teaching and public speaking, he would like to work with a private firm that conducts internal investigations. "Mueller is leaving the F.B.I. in very good shape," said David Margolis, a deputy associate attorney general and one of the most senior members of the Justice Department. But, Mr. Margolis said, "around here it is always one damn different thing after another," and now it will be Mr. Comey's job to solve those problems. Sarah Wheaton reported from Washington, and Michael S. Schmidt from Amagansett, N.Y.