1942 · The Battle of Midway

Within a few months of the Japanese attack on Pearl Harbor and America's entry into World War II, the U.S. Navy decrypted much of "JN 25," the Japanese Navy's main code -- an intelligence victory that gave American forces advance warning of a planned Japanese attack on the U.S. base at Midway Atoll. On June 7, 1942, the day after the U.S. victory at Midway, the Chicago Tribune ran an article by Stanley Johnston carrying the headline "NAVY HAD WORD OF JAP PLAN TO STRIKE AT SEA." Johnston's story did not explicitly mention the decryption of JN 25, but it included intercepted and decoded intelligence about Japanese naval forces that Johnston had obtained prior to the attack. That intelligence was so detailed that the government thought Japan would recognize that its code had been cracked. A grand jury was called to pursue a possible indictment of the Tribune under the Espionage Act, but the charges were dropped, possibly to avoid drawing further attention to the decryption.

1961 · The Bay of Pigs Invasion

During the Cold War, Fidel Castro's growing alliance with the Soviet Union following the 1959 Cuban revolution, in which Castro took power, raised deep U.S. concern. When The New York Times found out that the CIA was secretly funding and training Cuban exiles in Guatemala and Florida to overthrow Castro, the paper alerted the Kennedy administration that it was planning on running the story. President Kennedy asked the paper to back away, and the subsequent front page article, published on April 7, 1961 didn't mention that the planned invasion was "imminent" and left out all references to the CIA. Later, after the small U.S.-backed invading force was overwhelmed by Castro's forces and the U.S. government's role became public, President Kennedy told Times managing editor Turner Catledge, "If you had printed more about the operation, you would have saved us from a colossal mistake."

1971 · The Pentagon Papers

In June 1971, as the unpopular Vietnam war raged, The New York Times published the first in a planned series of articles about a classified 7,000-page study of the Vietnam conflict, the so-called "Pentagon Papers." The study had been ordered by Secretary of Defense Robert McNamara and was leaked to the Times and The Washington Post by Daniel Ellsberg, an analyst for the RAND Corporation. Attorney General John Mitchell telegraphed the Times to cease publication, citing the Espionage Act, a 1917 law that forbids the publication of national defense secrets. The administration quickly got a court injunction against the Times and the Post. The fight to lift the injunctions, led by Times counsel James Goodale, ended in a Supreme Court decision in favor of the newspapers' right to publish. The next day the two papers resumed publishing the Pentagon Papers. The New York Times Co v United States decision established the legal precedent against prior restraints on the press.

1975 · The Glomar Explorer

In 1968, Soviet submarine K-129 disappeared while carrying three nuclear missiles. The U.S. Navy located the wreck and the CIA, under orders from President Nixon, initiated the classified "Project Jennifer" to retrieve K-129 and the military secrets onboard. To carry out the operation, the government commissioned Howard Hughes to build the Glomar Explorer, a ship designed with a massive claw capable of lifting the sub some 17,000 feet into a holding bay. During the 1974 mission, a malfunction in the claw fractured the sub, allowing only a 38-foot section to be recovered. The Los Angeles Times ran a short story on Feb. 8, 1975 concerning a submarine retrieval, but did not mention the wider operation. CIA documents later released under the Freedom of Information Act show CIA Director William Colby and other intelligence officials brokered commitments from the Los Angeles Times, The New York Times, The Washington Post, National Public Radio and Parade magazine to withhold stories on Project Jennifer for several weeks in the interest of national security. However, several reporters suspected the CIA wanted to hold the story to avoid embarrassment rather than for national security purposes. Syndicated columnist Jack Anderson broke the Glomar story on his March 18 radio show and other news outlets followed immediately after.

1979 · The Progressive's H-bomb

The April 1979 issue of The Progressive magazine was originally planned to carry a cover story called "The H-bomb secret." The article's author, peace activist Howard Morland, claimed to have pieced together supposedly secret information about the hydrogen bomb's design "simply by reading and asking questions" and without illegally accessing any classified information. When the Department of Energy caught wind of the story, they offered to help the magazine's editors remove any references to classified material. The Progressive refused, and the government asked the court to intervene. On March 9, 1979, Federal District Judge Robert W. Warren restrained The Progressive magazine from publishing the story. The magazine fought to have the order lifted. Then, in September 1979, the Wisconsin newspaper Madison Press Connection and the Chicago Tribune published a letter from computer programmer Charles Hansen containing much of the same information as Morland's article. Within days, the government dropped its case and the U.S. Seventh Circuit Court of Appeals lifted the injunction. The Progressive ran the story intact, with a preface and technical corrections by Morland, in November.

1998 · Osama Bin Laden's Satellite Phone

Within days of the Al Qaeda-linked August 1998 bombings of two American embassies in East Africa, U.S. cruise missiles struck sites in Afghanistan and Sudan tied to Osama bin Laden. A day after those strikes, The Washington Times ran a profile of the Al Qaeda leader mentioning that he "keeps in touch with the world via computers and satellite phones … ." Soon after the attacks and the story, bin Laden stopped using his satellite phone, which the National Security Agency had been monitoring. A 2002 book by former Clinton administration officials alleged that the Washington Times' story tipped bin Laden off. The 9/11 Commission Report also said the article damaged efforts to track Al Qaeda.

The Washington Times disputed the allegations, and on Dec. 22, 2005, The Washington Post reported that the satellite phone had been mentioned by Time magazine in 1996, by CBS and CNN one day before the Times story, and by USA Today the same day. CNN's source was a 1997 interview with bin Laden himself.

2005 · The CIA's Secret Prisons

On Nov. 2, 2005, the first in a series of stories by intelligence correspondent Dana Priest exposed a network of secret CIA detention facilities for suspected terrorists that was set up in Eastern Europe, Afghanistan and Thailand. Drawing on anonymous sources within the federal government and intelligence agencies, Priest documented how the agency placed captives into the "black sites" or handed them over to countries such as Egypt, Jordan, Morocco and Afghanistan for interrogation in order to skirt U.S. and international rules governing the treatment of prisoners. The Post discussed the story with government officials before publishing it and omitted sensitive information at their request. Nonetheless, Congressional Republican leaders Trent Lott and Dennis Hastert called for a joint congressional investigation on Nov. 8, and a leak investigation was opened by the Department of Justice.

2005 · The NSA's Domestic Surveillance

The front page of the Dec. 16, 2005 New York Times reported that in 2002, the National Security Agency began monitoring the international phone calls and e-mails of some U.S. residents, in secret and without a court warrant, to uncover possible connections to terrorist organizations. The Times had held the story for a year at the government's request, and its publication on the same day as a scheduled vote on the renewal of the Patriot Act led The Washington Post, Washington Times and others to question the paper's motives. On Dec. 17, President Bush acknowledged authorizing the program, defended its legality and called the revelations "shameful." Later that month, the Department of Justice opened an investigation into who had leaked information. U.S. District Judge Anna Diggs Taylor ruled in August of 2006 that the program was illegal, and although the Bush administration expected the decision to be overturned on appeal, on Jan. 17, 2007, Attorney General Alberto Gonzales announced that the program would be overseen by a Foreign Intelligence Surveillance Act (FISA) court.

2006 · The SWIFT Financial Monitoring Program

On June 23, 2006, The New York Times revealed that in 2001, the Bush administration began secretly monitoring financial transactions between people within the U.S. and others overseas. Using what the Times called "broad administrative subpoenas," the CIA and Treasury Department accessed files at the Society for Worldwide Interbank Financial Telecommunication (SWIFT), a Belgian financial hub, to pursue leads to terrorists. President Bush called the Times disclosure "disgraceful," the House passed a resolution condemning the press outlets that ran the story, and Rep. Peter King (R-N.Y.), chairman of the House Homeland Security Committee, wrote the Attorney General formally requesting that the Times be investigated for possible criminal prosecution under the Espionage Act -- the same law the Nixon administration had used in trying to prevent the publication of the Pentagon Papers. New York Times Executive Editor Bill Keller defended the decision, and said that he took the government's arguments against publishing seriously but found them unconvincing. Times Public Editor Byron Calame initially supported the Times' story, but in October of 2006, he withdrew that support, citing the care with which the government executed the program. The program remains active. However in February 2007, an EU regulatory body said that SWIFT's cooperation is a violation of privacy restrictions and urged the European Central Bank to intervene.