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The Church of Scientology, in its efforts to investigate and attack its "enemies," kept files on five Washington federal judges, Sen. Edward M. Kennedy, other congressmen, Jacqueline Onassis, the Better Business Bureau and the American Medical Association, according to Scientology documents in the possession of federal investigators.

The Scientologists' files, summarized in a 525-page inventory filed in court by the federal government, were in many cases marked "Eyes Only," "Top Secret," "Enemy Names" and "Battle Plans." Their contents were coded with phrases like "Operation Cut Throat," "Espionage" and "Operation Big Mouth."

The documents, which were seized under subpoena by federal agents in raids of Scientology offices here and in Los Angeles last summer, include orders from top Scientology officials to investigate and attack certain government agencies, private businesses and individuals.

Among other Scientology property seized in the raids were memos on how to obtain false identities and tap telephones, a lockpicking kit, electronic eavesdropping equipment, two 22-caliber pistols and a leather blackjack, according to the government inventory filed in federal court in Los Angeles.

Federal investigators studying the thousands of pages of seized Scientology papers also have found secret CIA documents, "apparently original" Internal Revenue Service documents, and confidential letters between presidential Cabinet members including one letter that apparently was drafted but never sent.

Federal prosecutors are submitting some of the seized documents to a federal grand jury here that is investigating the Scientologists. A government affidavit filed in connection with last summer's searches quoted a former high-ranking Scientology official who said the Scientologists were waging an "all out attack" on the government through infiltration, burglaries, theft of government documents and buggings.

The Church of Scientology has answered that it has broken no laws and has in fact been the victim of a government conspiracy to destroy it. Government documents in its possession, according to Scientology officials, were legally obtained through the Freedom of Information Act (FOIA). Some of the documents seized by the government had been marked by the Scientologists "FOIA," according to the inventory, while others were marked "non-FOIA."

Last night a spokesman for the Scientologists accused the FBI of "leaking erroneous data" in an effort to influence ongoing court proceedings in which the Scientologists are fighting to have their documents returned.

"They [FBI] are twisting facts to attribute to the church dirty tricks which they [FBI] have specialized in for years, which continues to this day," the spokesman said. "The Washington Post is allowing itself to be used as a mouthpiece for these lies and half truths."

The Washington Post reported recently that, according to informed sources, some of the seized Scientology documents indicate that church members staged a bogus hit-and-run accident in Rock Creek Park here in an attempt to compromise a visiting mayor who had opposed the Scientologists in Florida. The Post also reported that, according to those same sources, the church had forged a rough draft of an embarrassing news story under a Florida reporter's name to undermine his credibility and had faked a bomb threat to frame the author of a book critical of Scientology.

According to both the government affidavit and its inventory of the seized Scientology documents, top Scientology officials were aware of and participated in the campaign to silence critics of Scientology.

These officials, according to the court documents, include Henning Heldt, head of the Church of Scientology's Guardian Office in this country, and Mary Sue Hubbard, wife of Scientology founder L. Ron Hubbard and the second-ranking person in the Scientology heirarchy.

According to the government affidavit, the Guardian's Office, one of the two major divisions of the Church of Scientology, is responsible for carrying out covert operations to acquire government documents and "to discredit and remove from positions of power all persons whom the Church considers to be its enemies."

According to the government inventory of the seized documents, Scientologists gathered information on the personal habits and courtroom conduct of U.S. District Court judges Oliver Gasch, Gerhard A. Gessel, Joseph C. McGarraghy and John J. Sirica, and U.S. Court of Appeals judge Carl McGowan, all of whom have have handled some aspect of cases brought by or against Scientologists here.

Some of the information was obtained from the judges' private files, according to the inventory. Other bits came from interviews in which Scientologists masquaraded as students or reporters, a tactic that Scientology documents refer to as "suitable guise" interviews.

The material gathered ranges from assessments of the judges' reactions to various legal tactics to Judge Gasch's real estate transactions.

The files also include, according to the inventory, a five-page "investigation" of Sen. Edward M. Kennedy (D-Mass.) and references to an acquaintance of Kennedy's named Helga Wagner.

Kennedy's spokesman, Tom Southwick, said yesterday that the Scientologists might have been interested in Kennedy because they oppose portions of his criminal code revisions that would allow judges to refer defendants to psychiatrists.

The same memo that mentions Kennedy and Helga Wagner, according to the government, also says that "Wagner and Jackie Onassis (sic) have known each other for approximately eight years," and says that telephone conversation with Onassis was to interest her in the church.

A spokesman for the scientologists said the files on the judges "are nothing more than the files which would be maintained on judges in every law office in the United States."

According to the government inventory, the Scientologists kept extensive files on the American Medical Association, the Better Business Bureau and the American Psychiatric Association, all of which had investigated Scientology or published articles about it.

The Scientologists' investigation included, according to documents, the infiltration of several Scientologists into the AMA as employes. One, a secretary, had access to meetings of the AMA's board of directors.

During 1975, confidential AMA documents were leaked to the press by then unknown sources, one of whom was nicknamed "Sore Throat" by the press. The leaked information led to investigations of the AMA by the Internal Revenue Service, U.S. Postal Service, several congressional committees, Ralph Nader and the press.

An AMA spokesman characterized the leaks as "like death by a thousand cuts." The organization frantically searched for the sources and ultimately accused the Church of Scientology. Scientology spokesmen dismissed the accusation at the time, calling it "illustrative grasping in the dark to cover their own crimes."

A team of 20 FBI agents has spent weeks cataloging the thousands of Scientology documents. According to the government inventory, they have found file folders and operations with the code names "Billy's Baby," "Vanguard," "Hunter," "Fleece," "Starpoint," "Amber," "Pink In," and 'Lantern.'

One church document, dated Jan. 20, 1977, is entitled, "The Correct Use of Codes." There is no further elaboration in the government summary.

The Scientologists kept files on scores of people and dozens of Congressmen, according to the inventory.

Folders included files on such disparate institutions as the Glendale City Council, Letterman's Army Medical Center, Folsom Prison, the Albany Chamber of Commerce, Carnegie Hall, the Pasadena Department of Finance and the King County, Wash, Department of Public Safety.

In the organization's files are memos, letters, documents and teletypes, many of them confidential, dealing with intelligence matters involving the Justice Department, the Internal Revenue Service, the Treasury Department, and the Bureau of Alcohol, Tobacco and Firearms, according to the government inventory. One item seized is a draft of a letter from a former attorney general to a former secretary of the Treasury marked "Not Sent."

Also there are references in seized Scientology memos to "D.C. Police Plants Debriefs," and "FDA Plant Debriefs, 1959," according to the inventory. The "debriefs" notations are references to reports filed by informers for the FDA and D.C. police that went to Scientologists, according to informed sources.

The government has possession of the organization's files dealing with several men who were D.C. policemen and with local law firms, including Williams and Connolly, and Feldman, Ginsburg and Bress, according to the inventory. Both have had some connection with Scientology court cases.

The government inventory includes brief descriptions of a number of documents, with words in quotation marks taken directly from the documents, according to the government. In most cases the descriptions are brief, with no elaboration.

The inventory also includes the following:

* A one-page confidential executive directive bearing the stamp "highest priority" and dated April 13, 1976, listing agencies "toward which our attack vector should be aimed." The list includes the State Department, Interpol, the FBI, Post Office, Justice Department, IRS, CIA and Treasury Department.

* A one-page document dated Nov. 6, 1975, entitled, "IRS: Zapping Them."

* A four-page memo on obtaining false identification.

* A three-page memo on obtaining false birth certificates.

* A memo on the "Vetting Hat Addition" which deals with the penetration of nongovernment organizations and the tapping of phone conversations.

* A nine-page report designated priority regarding "Operations on enemies Sableman, Orsini and Bob Snyder." Reporters with these names wrote stories critical of Scientology.

* A seven-page memo dated Dec. 2, 1974, entitled "The Tailing and Following of Agents: What to Do."

* A manila folder entitled Operation Cut Throat containing six documents regarding the infiltration of the Better Business Bureau of Greater St. Louis.

* A confidential Better Business Bureau report entitled "The Church of Scientology of Boston."

Raymond Banoun, an assistant United States Attorney and the chief investigator in the government's probe into Scientology, declined to elaborate on the church documents beyond what is in the inventory.

Scientologists have contended in court documents, press releases and interviews that they are victims of a 20-year campaign of harassment by the federal government, which is attempting to suppress their religion.

After recent articles in The Post about their alleged activities, scientology spokesmen held rallies and put out news releases announcing that the organization had been "monitoring" government activities in order to find "government illegalities and cover-ups" and make them public.

The spokesmen announced the formation of a new group, American Citizens for Honesty in Government, and called on "every honest government employee" to report improprieties to the "ACHG Ethics Committee."

Scientology has been the subject of controversy since its founding in the late 1940s. It has been called quackery, and endorsed as a means to peace of mind.

The movement was founded by L. Ron Hubbard, a former science fiction writer who spread his gospel in a best-selling book, "Dianetics: The Modern Science of Mental Health."

Scientology professes to be a religion in which people can be "cleared" of troubling experiences through sessions with "auditors" or counselors. Fees for this auditing and courses in the movement's philosophy can cost thousands of dollars.

Government interest in Scientology files increased last year after a high ranking organization official, Michael Meisner, began telling the FBI and prosecutors about Scientology covert operations and documents. Meisner had been sought by the FBI in connection with his illegal entry into the U.S. District Courthouse here. He has since become a key government witness and is under protective custody, according to informed sources.

Meisner has told the government that Scientology officials hid him while he was a fugitive and then placed him under 24-hour guard when he tried to return to Washington. At one point, he has said in an affidavit, he was moved from one building to another while handcuffed and gagged.

According to the government inventory of Church documents, a number of top Church officials, including Henning Heldt and Mary Sue Hubbard, talked about Meisner's situation while he was a fugitive. One memo, found in Heldt's desk, begins "Dear Mary Sue, Herb is threatening to return to D.C."

"Herb," Meisner has sworn, was a code name for him. Other documents, with cross references to Herb and Meisner, confirm that, according to informed sources.

According to Meisner's sworn statements, organization officials believed it was essential for the operation and security of Scientology to keep detailed records.