WASHINGTON, Oct 10 — Last fall, federal agents raided the home and office of Robin L. Raphel in search of proof that she, a seasoned member of America’s diplomatic corps, was spying for Pakistan. But officials now say the spying investigation has all but fizzled, leaving the Justice Department to decide whether to prosecute Ms. Raphel for the far less serious charge of keeping classified information in her home.
The fallout from the investigation has in the meantime seriously damaged Ms. Raphel’s reputation, built over decades in some of the world’s most volatile countries.
If the Justice Department declines to file spying charges, as several officials said they expected, it will be the latest example of American law enforcement agencies bringing an espionage investigation into the public eye, only to see it dissipate under further scrutiny. Last month, the Justice Department dropped charges against a Temple University physicist who had been accused of sharing sensitive information with China. In May, prosecutors dropped all charges against a government hydrologist who had been under investigation for espionage.
Ms. Raphel, in negotiations with the government, has rejected plea deals and has been adamant that she face no charges, according to current and former government officials, particularly because the Justice Department has been criticized in recent years for handing out inconsistent punishments to American officials who mishandle classified information.
Both the Justice Department and a lawyer for Ms. Raphel, Amy Jeffress, declined to comment.
The Raphel case has also been caught in the crosswinds of America’s tempestuous relationship with Pakistan, a strong Cold War alliance that has frayed since the Sept. 11, 2001, attacks amid recriminations between Washington and Islamabad. Ms. Raphel has for decades been at the center of shaping American policy toward Pakistan, and she has maintained close ties to Pakistani officials even as many of her colleagues became disenchanted with what they saw as Islamabad’s duplicity in the fight against terrorism.
Against that backdrop, the federal investigation has delved into the murky world of international statecraft, where diplomats exert influence through a careful dance of trading, sharing and eliciting information. Some American investigators viewed Ms. Raphel’s relationships with deep suspicion.
Those suspicions became a federal investigation last year when American officials, while eavesdropping on a Pakistani government official, intercepted a conversation that seemed to suggest that Ms. Raphel, an adviser at the State Department, was passing American secrets to Pakistan. The reason for the eavesdropping is unclear, but the government routinely listens to the phone calls and reads the emails of foreign officials.
After months of secret surveillance, the investigation into Ms. Raphel spilled into the public when agents searched her home and her State Department office last October. She was quickly stripped of her security clearances and left in the dark about the precise origins of the federal investigation. Her friends said that the investigation had taken a deep emotional toll.
“Sometimes the whiff of scandal can be worse than any actual scandal,” said Husain Haqqani, a former Pakistan ambassador to Washington who has known Ms. Raphel for years. “More people hear that you were investigated than care to know you were cleared or never actually charged.”
American officials will not discuss what classified information the investigators found in Ms. Raphel’s home. The current and former American officials who discussed the case did so on the condition of anonymity because they were not authorized to talk about it publicly.
Over the years, the stories of American officials mishandling classified information have at times seemed as peculiar as they were serious. John P. O’Neill, a counterterrorism specialist for the F.B.I., once lost a briefcase full of government secrets in a Florida hotel. Samuel R. Berger, the national security adviser to President Bill Clinton, stole classified documents from the National Archives and hid them under a construction trailer. As attorney general, Alberto R. Gonzales took material about the nation’s warrantless wiretapping program home with him.
One C.I.A. director, John M. Deutch, stored classified information on his home computer. Another C.I.A. director, David H. Petraeus, shared his highly classified journals with his mistress, then lied to the F.B.I. about it. Hillary Rodham Clinton used a private email system when she was secretary of state that investigators say contained classified information, although Mrs. Clinton and the State Department say the information was not marked as classified.
The punishment for mishandling classified information has varied wildly. Mrs. Clinton has not been charged with wrongdoing. Mr. Berger pleaded guilty to a misdemeanor. Mr. Deutch received a pardon from Mr. Clinton and was never charged. Mr. Gonzales and Mr. O’Neill were not charged. In the most recent case, the Justice Department allowed Mr. Petraeus to plead guilty to a misdemeanor, despite strong objections from investigators. That deal was so contentious that the F.B.I. director, James B. Comey, personally appealed to the attorney general, Eric H. Holder Jr., and said that Mr. Petraeus’s crimes warranted felony charges, according to two government officials involved in the case. F.B.I. agents are still angry about that decision and say it set a standard that will make it harder to bring cases in the future.
In discussions with prosecutors, according to several government officials, Ms. Raphel and her lawyer have cited the Petraeus case as the vital precedent. If passing secrets — including notes on war strategy and the names of covert officers, which Mr. Petraeus shared — and lying about it amount to a misdemeanor, then, Ms. Raphel says, she should not face any charges.
Some American investigators remain suspicious of Ms. Raphel and are loath to abandon the case entirely. Even if the government cannot mount a case for outright spying, they are pushing for a felony charge related to the classified information in her home. Several officials acknowledged, however, that the case would be difficult to prosecute because it would require intelligence agencies to declassify information and would probably reveal secrets about American surveillance of foreign officials.
Felony charges for improperly taking and storing classified information, while not espionage in the common sense of the word, would be filed under the Espionage Act and could expose Ms. Raphel to years in prison — a far stiffer penalty than Mr. Petraeus and others received.
The news of the investigation has shaken policy circles in Washington, where Ms. Raphel has been a fixture as a diplomat, a South Asia expert in the private sector, and a lobbyist. She began her career as a C.I.A. analyst but moved quickly to the State Department, which sent her to Islamabad in the mid-1970s. It was during this posting that she met and married Arnold L. Raphel, another foreign service officer. In 1988, while he was America’s ambassador to Pakistan and after he and Ms. Raphel had divorced, Mr. Raphel was killed in a plane crash with the Pakistani president, Mohammed Zia ul-Haq.
During the Clinton administration, Ms. Raphel served as the assistant secretary of state for South Asia, and then ambassador to Tunisia. In the George W. Bush administration, she was the State Department’s coordinator for reconstruction in Iraq, where she tried to guide the war-torn country toward a stable government and economy. After retiring from the government in 2005, she joined Cassidy & Associates, a Washington lobbying firm that represents the Pakistani government, among other clients.
At the start of the Obama administration, Richard C. Holbrooke, the State Department’s special representative for Afghanistan and Pakistan, reached out to Ms. Raphel to work with him. She quit her lobbying job and was sent as a State Department contractor to the American Embassy in Islamabad, where she helped disburse American aid to Pakistan. Until the F.B.I. investigation, she continued to work on contract as an adviser on Pakistan and Afghanistan.
During her long career working on Pakistan issues, Ms. Raphel has seen the country go from being one of America’s most steadfast Cold War allies — and a partner in the 1980s effort to train Afghan fighters to expel Soviet troops from Afghanistan — to being something of a pariah to Washington. Although Pakistan pledged support for the campaign against Al Qaeda and the Taliban after the Sept. 11 attacks, senior members of both the George W. Bush and Obama administrations became convinced that Pakistani soldiers and spies were aiding the Taliban and other militant groups by attacking American troops in Afghanistan.
For their part, Pakistani officials stoked fury in the country about the C.I.A.’s campaign of drone strikes and what they came to see as the agency’s expansion operations in Pakistan.
As relations between the two countries deteriorated, Ms. Raphel was considered one of Pakistan’s few remaining supporters in the top echelon of American government. This earned her enemies among government officials in India, Pakistan’s archrival, but also among colleagues who considered her too sympathetic toward an unreliable ally.
“I don’t think it was very fashionable to say, ‘I think the Pakistanis have a point,’ but Robin did that,” said Cameron Munter, the former American ambassador to Pakistan who oversaw Ms. Raphel’s work in Islamabad