The cause was pneumonia, said his daughter Jeanne Theoharis.

Theoharis, a professor emeritus of history at Marquette University in Milwaukee, was widely considered the dean of FBI scholars – a master researcher admired by journalists, activists and fellow historians for shedding light on one of the nation’s most prominent but taciturn law enforcement agencies.

“Doing FBI history research is real detective work, ironically enough, and Athan Theoharis was a master at getting behind the bureau’s veil of secrecy,” said Douglas Charles, a Pennsylvania State University history professor who researches the bureau and studied under Theoharis. “In my own research, I’ve used all of these tactics he devised with success. . . . No scholar knew the FBI better than he did.”

While other historians examined individual cases or FBI targets, Theoharis focused on unraveling the agency’s byzantine filing and records procedures. His research led to the discovery of the “secret files” of Director J. Edgar Hoover and his top deputies, who kept sensitive files in their own offices, outside of the bureau’s “official” filing system. Some documents, intended for destruction, were simply labeled “Do Not File.”

Theoharis obtained tens of thousands of documents related to illegal wiretaps, mail openings and break-ins. Some showed that the FBI had gathered embarrassing material about top officials, including President Dwight D. Eisenhower, and broke into the office of left-wing organizations such as the American Youth Congress, where it photocopied correspondence with first lady Eleanor Roosevelt.

Other files revealed an investigation into communist infiltration in Hollywood, where Ronald Reagan – then president of the Screen Actors Guild – was recruited as an FBI informer in the 1940s and instructed to report on actors who followed “the Communist party line.” Theoharis also exposed a secret, quarter-century partnership between the FBI and the American Legion, in which tens of thousands of Legionnaires were enlisted to report on other citizens.

In an email interview, Charles said that Theoharis came up with “creative ways” to acquire FBI files, including by locating documents that were shared with the White House and ended up at presidential libraries, which released them with fewer redactions. He sued to obtain some documents and raised more than $30,000 from nonprofit organizations to pay for FBI research and copying fees.

As he reviewed the files, Theoharis began to argue that the bureau’s reputation for catching gangsters, spies and terrorists was grossly exaggerated, and that its surveillance programs threatened civil liberties. While he noted that presidents such as Franklin D. Roosevelt had wielded the FBI as a political tool, ordering the bureau to investigate opponents, he assigned much of the blame for its improprieties to Hoover, who ruled the FBI for 48 years until his death in 1972.

“Hoover was an insubordinate bureaucrat in charge of a lawless organization,” he told the Milwaukee Journal in a 1993 interview. “He was also a genius who could set up a system of illegal activities and a way to keep all documentation secret for many years.”

Theoharis chronicled Hoover’s FBI in books including “The Boss” (1988), with co-author John Stuart Cox, and “From the Secret Files of J. Edgar Hoover” (1991), offering commentary for a sweeping collection of FBI documents. Historian Arthur Schlesinger Jr. called the latter volume “a grimly fascinating – and profoundly disturbing – self-exposure by one of the false American deities of the 20th century.”

Along with other FBI historians, Theoharis pushed back against rumors that Hoover was a closeted gay man who liked to dress as a woman. He sought to focus attention on the FBI as an institution, much as he had previously argued that the term “McCarthyism” was a misleading label for the anti-communist campaign that emerged under President Harry S. Truman.

“He’s somebody who resists ways in which we try to personalize abuses of power,” said his daughter Jeanne, a political science professor at Brooklyn College who partnered with him to write a 2002 book about civil rights and liberties. In a phone interview, she added that Theoharis had sought to help journalists, scholars, political activists and even “random high school students in Maine” obtain FBI files using FOIA requests.

“It was a little bit like a religion for him,” she added, “a religion of open access and civil liberties.”

The second of five children, Athanasios George Theoharis was born in Milwaukee on Aug. 3, 1936. His mother and father, a Greek immigrant, ran a diner out of the first floor of their home, where Athan worked as a boy. At 16, he earned a scholarship to the University of Chicago.

Theoharis initially studied political science, and received bachelor’s degrees in 1956 and 1957, a master’s degree in 1958 and a doctorate in history in 1965. In books such as “The Yalta Myths” (1970) and “Seeds of Repression” (1971), he examined the Truman administration and the 1945 Yalta Conference between the heads of the United States, the Soviet Union and Britain.

He taught at what is now Texas A&M University, Wayne State University in Detroit and the College of Staten Island before joining Marquette in 1969. Two years later, he published “Thirty Years of Wire Tapping,” an article in the Nation that attracted the attention of the Church Committee, a U.S. Senate committee formed in 1975 to investigate abuses by the FBI and other U.S. national security agencies.

Theoharis was soon hired as a consultant for the committee. When he received a limited security clearance for his work, it was as though “the curtains parted,” his daughter recalled. He spent the rest of his career trying to peer deeper behind those curtains, working for decades out of a cluttered office that he filled with reams of newspaper clippings and FBI files.

After the Sept. 11, 2001, terrorist attacks, he tried to sound the alarm on secrecy and surveillance, arguing against the expansion of the FBI’s domestic spying programs in books such as “Abuse of Power” (2011). He later joined former staffers and members of the Church Committee in calling for the creation of a new committee to investigate U.S. intelligence practices.

His wife of 53 years, the former Nancy Artinian, died last year. In addition to his daughter Jeanne of Brooklyn, survivors include another daughter, the Rev. Liz Theoharis of Manhattan, the co-chairwoman of the Poor People’s Campaign; a son, George Theoharis of Syracuse, a professor of educational leadership at Syracuse University; a brother; two sisters; and five grandchildren.

Well into the digital age, Theoharis banged away at an old typewriter and abstained from email, calling himself “technologically illiterate” in an interview with Milwaukee Magazine. He served on the board of the Wisconsin American Civil Liberties Union and obsessively followed college basketball, organizing a weekly pickup game with students and colleagues for decades. Even after he retired in 2006, the game continued, along with his research.

“This kind of research is problematic,” he said in an interview at the time with the student-run Marquette Tribune. “You can decide when you want to begin, but you can’t determine when you’ll end. The length of getting the records, in some cases, can take years. Just the other day someone called about a request I made in 1998 about Richard Nixon, asking if I was still interested.”