The threat from soviet strategic weapons and the need to accurately assess Moscow's intentions and capabilities were never more important than in the 1962 Cuban Missile Crisis, the most dramatic episode in the decades-long confrontation between the United States and the USSR.

Soviet premier Nikita Khrushchev (1894–1971) was famous for his public bluster, but U.S. analysts did not appreciate the extent to which he was privately concerned that his country was at a disadvantage in the rivalry between the superpowers. For example, Khrushchev knew that, after a slow start, the United States had been able, by the early 1960s, to surpass the USSR in the production of strategic nuclear weapons and delivery systems. In addition to sites in the United States, these enormously destructive weapons were deployed on bases in Western Europe and Turkey, and thus, from Khrushchev's perspective, were able to surround the USSR. In addition, American officials had tried in 1961 to overthrow communism's only outpost in the Western Hemisphere, the regime of Fidel Castro (1926–) in Cuba.

To address these issues, Khrushchev launched a massive and daring undertaking in the spring of 1962. First, the USSR would publicly provide large amounts of conventional weapons to Cuba, including fighter aircraft, tanks, patrol boats, surface-to-air missiles (SAMs), and radar. Second, the Soviets would secretly send several dozen medium- and intermediate-range ballistic missiles (MRBMs and IRBMs) to Cuba, along with a large contingent of Soviet troops to protect them.

Air power had not been a decisive factor in world war i, but technological improvements in the 1920s and 1930s had made it a matter of great concern. Theorists, such as the Italian Giulio Douhet (1869–1930), believed that massive bombing attacks from the air would be the decisive weapon of the next war. In Britain, the leader of the Conservative Party, Stanley Baldwin (1867–1947), claimed that “the bomber will always get through.” Even in popular culture, movies such as The Shape of Things to Come envisioned a world in which airpower would be of decisive importance. Military planners trying to design and implement defenses, as well as civilian officials with budgetary responsibilities, grappled with how to assess a technology that had never been used extensively and was constantly advancing. The problem was particularly acute when trying to estimate the threat from Germany.

One of the provisions of the Treaty of Versailles had been that Germany was not to have an air force. Given the increasing importance of air power, however, the postwar German democratic governments fostered a limited secret aerial rearmament in defiance of the treaty. In 1933, Adolf Hitler (1889–1945), the head of the National Socialist (Nazi) Party who had made criticism of the treaty a key element of his foreign policy, became Chancellor of Germany and soon established a dictatorship. In addition to other rearmament efforts, he continued and accelerated clandestine efforts to build war planes.

In stark contrast to that of the previous 3,000 years, intelligence analysis in the nineteenth and twentieth centuries was transformed by three factors: bureaucracy, technology, and psychology.

From the nineteenth century onward, support to decision making in government was increasingly done by large, permanent organizations. These large organizations were characterized by hierarchical structure and division of labor, and they had both strengths and weaknesses. As demonstrated in factories, they could handle massive volumes of work, especially of a routine nature, but the flow of information up and down through the various layers of hierarchy could also lead to distortion and delay. Soon the bureaucratic style of organization was being used in armies, governments, political parties, and other functions. It was only a matter of time before it spread to intelligence analysis.

Another significant development in the nineteenth century was the increasing application of science to business, weaponry, law enforcement, and other fields. There were various versions of the scientific method, but basically the main steps were to formulate a question, propose one or more hypotheses that could answer the question, gather relevant facts, use those facts to test the hypotheses, and then accept, adjust, or abandon the hypotheses based on the results of the tests. This procedure produced a number of benefits, including new medicines and commercial products. Such systematic inquiry could also be of assistance in intelligence analysis.

On september 25, 1992, china tested a new type of nuclear bomb. For the next several years, analysts and scientists in the United States studied data on the test; in time, scientists at the Los Alamos nuclear labs, where the first U.S. nuclear weapons had been developed, became worried that the test showed that the Chinese were developing dramatically smaller warheads. If true, this represented a dramatic potential increase in China's nuclear capabilities. Miniaturized warheads could go on mobile missiles that would be harder to detect, and eventually they could be used as multiple warheads on strategic intercontinental missiles. The scientists were concerned that the Chinese could only have made such progress if they had based their warhead designs, in part, on nuclear weapons technology stolen from the United States. These fears appeared to be confirmed by a 1995 Central Intelligence Agency (CIA) report, based on 1988 documents, stating that the new Chinese bomb was similar to American technology.

Counterespionage investigations are among the most daunting challenges for intelligence analysts. It can be difficult to determine for certain, especially over the short term, whether espionage has even taken place. Spies are often experienced professionals who know how to cover their tracks. Even if there are well-founded suspicions, coming up with evidence that can hold up in court can be demanding. In any case, the investigation is almost certain to require considerable amounts of time, money, and expertise, with an uncertain outcome.

According to history of the peloponnesian war, by thucydides (c. 460–c. 395), who was an eyewitness, there was a stalemate in the war in the late fifth century BCE. After a decade and a half of fighting between Athens and its allies on one side, and Sparta along with its allies on the other, neither side had prevailed and there was a shaky peace in place on the Greek mainland. Then a plea for help arrived from a small city–state in western Sicily, Egesta (also rendered as Segesta), which was an Athenian ally. Egesta was doing poorly in a local conflict with its neighbor Selinus, which was backed by Syracuse, the dominant city–state in the eastern part of the island and a potential ally of Sparta. To make the request for assistance attractive, the Egestaeans offered to pay for Athenian support.

Athens had a democratic government, and when the appeal from Egesta had arrived in Athens there was a vigorous public debate in the assembly about how to respond. Some saw this as an opportunity to expand Athenian influence on Sicily and undermine Sparta. Others were wary about making a serious commitment so far away – Sicily was 600 miles (960 kilometers) from Athens – while the rivalry with Sparta had not been resolved. As the debate continued, it became clear that there was an important question that could be addressed by intelligence analysis: The Egestaeans had offered to make a large financial contribution, but did they really have the means to provide significant assistance?

On october 2, 2001, a photo editor for american media inc. checked into a hospital in Boca Raton, Florida (which is not far from Fort Lauderdale and Delray Beach), complaining of flulike symptoms. After a series of tests, doctors diagnosed that he had inhaled spores of anthrax, a disease not seen in its natural form in the United States since 1976, and one of the most destructive biological warfare agents. The photo editor died on October 5, and, in the meantime, a second employee of American Media was hospitalized with symptoms of inhalation anthrax. An investigation revealed that the anthrax spores had reached the American Media offices through the mail, but the original letter and envelope had since been destroyed, and it was impossible to determine any further details about who had mailed it. Postal officials decided against closing down the postal system because they were concerned that such a move might generate panic.

Because of the unusual nature of the disease and the timing – just three weeks after the 9/11 attacks – terrorism was the initial hypothesis. One of the employees of a tabloid published by American Media recalled that the paper had recently published an article that had mocked Osama bin Laden. Another editor at American Media had a spouse who was a real estate agent who had rented apartments to several of the future hijackers.