WASHINGTON -- On Oct. 21, 2014, Robin Raphel, a former assistant secretary of state, got an urgent call from her daughter, who said that something had triggered the burglar alarm at home. When Raphel arrived, she found FBI agents searching through her files and other personal materials.

Raphel frantically telephoned her office at the State Department to ask what was happening; colleagues said they had been instructed not to speak with her. Agents were already rifling her desk at State, and putting up yellow tape to warn off workmates.

Raphel's voice still shakes with emotion as she recalls that afternoon. The FBI search warrant said she was being investigated under 18 U.S. Code Section 793(e), a criminal statute that covers illegal gathering or transmission of national-security information and is used in espionage cases. The warrant offered no other details.

Justice Department officials privately told attorneys and journalists that they had probable cause, based on intelligence intercepts and other sources, to believe that Raphel, one of the government's leading experts on South Asia, had been spying for Pakistan. They also revealed that they had found classified documents in the search of Raphel's home.

The government's case collapsed in March, when the Justice Department informed Raphel's attorneys it wouldn't prosecute her, either for espionage or improper retention of the documents. That seems a wise exercise of judgment -- but it came way too late.

The case leaves behind some disturbing questions about how a diplomat with nearly 40 years' experience became the focus of a career-shattering investigation -- apparently without anyone seeking clarification from knowledgeable State Department officials about her assignment to open alternative channels to repair the badly strained relationship with Pakistan.

"If the Bureau had talked to senior people at State who were knowledgeable about her work, I believe they would never have launched this investigation," argues Jeff Smith, a former CIA general counsel who was one of Raphel's attorneys.

The threat that government surveillance and national-security investigations pose for private citizens has been hotly debated for the past decade. Less understood is the wrongful damage done to government officials themselves when they fall into the dragnet. Raphel's experience is a case study in what can happen when the government launches a toxic investigation without adequate due diligence.

"The FBI's investigation of me was flawed from the beginning because they had a fundamental misunderstanding of what diplomats do," Raphel explained to me. "I was never told what triggered the investigation, but I am convinced it was a misreading of raw intelligence by persons who simply did not understand the context."

Three of Raphel's supervisors at State's office of the Special Representative for Afghanistan and Pakistan, known as SRAP, explained Raphel's mission when she became a special adviser in 2011 after leaving a post in Islamabad overseeing U.S. assistance there. At that time, the relationship between Washington and Islamabad was poisonous, with deep mistrust among intelligence and military officials. Raphel's assignment was to "augment existing channels" at the embassy by talking to Pakistani friends and contacts, explained one supervisor.

Raphel, with decades of experience dealing with Pakistan, added an extra dimension. A second supervisor said her mission was to "double track" the messages being passed by the embassy. A third recalled that in 2011 and 2012, "military and intelligence channels were closed. It was the other channels that kept the relationship on life support and helped nurture it back."

Dan Feldman, Raphel's last boss at SRAP, says the case shows that other agencies need to better understand diplomacy: "I wish there had been better and more coordinated knowledge about the nature and importance of diplomatic channels, and what it entails for diplomats to be effective in pursuing critical national security priorities."

The case had a "chilling effect" on other diplomats who feared they might be next, a half-dozen State Department officials told me. But Raphel's colleagues stood behind her, even when the investigation was still active. Beth Jones, another former assistant secretary of state, organized a legal defense fund last summer. The fund raised nearly $90,000 from 96 colleagues and friends, many of whom, recalls Jones, voiced the fear: "There but for the grace of God go I."

Diplomats often go last in our national-security parade. People cheer at ballparks when they see soldiers and sailors. They stand in line to watch movies about snipers and special-forces operators. But a diplomat's reward for years in danger sometimes seems to be a congressional or FBI investigation for security lapses. That's wrong. Raphel and many hundreds of colleagues deserve better support.

(c) 2016, Washington Post Writers Group