From War History Online:
Many events in history have been changed because of covert missions undergone by the military or by secret organizations led by the government. As a result of such activities, there have been discoveries made, conspiracies disclosed, injustices done, lives killed, and governments changed as a result of keeping everything concealed from public knowledge.
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1. The Underground Nuclear Ice City
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Sometimes history is just a little bit weirder than science fiction.
After the military takeover, Camp Century was converted into a giant ice-bound missile silo. The goal was to store approximately 600 nuclear missiles in the base. Project Iceworm was the code name for a top-secret United States Army program during the Cold War to build a network of mobile nuclear missile launch sites under the Greenland ice sheet. The ultimate objective of placing medium-range missiles under the ice — close enough to strike targets within the Soviet Union — was kept secret from the Danish government. To study the feasibility of working under the ice, a highly publicized “cover” project, known as Camp Century, was launched in 1960. However, unsteady ice conditions within the ice sheet caused the project to be cancelled in 1966.
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Details of the missile base project were secret for decades, first coming to light in January 1995 and resulting in a political scandal, when the Danish Foreign Policy Institute (DUPI) was asked by the Folketing (Danish Parliament) to research the history of nuclear weapons in Greenland during the Cold War.
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In the aftermath of World War II American Intelligence launched Operation Paperclip as a covert attempt to recruit the scientists of Nazi Germany for employment in the United States. It turned out to be quite successful.
3. Operation Anthropoid
Operation Anthropoid was the code name for the assassination attempt on Nazi Officer Reinhard Heydrich. The operation was carried out in Prague on 27 May 1942 after having been prepared by the British Special Operations Executive with the approval of the Czechoslovak government-in-exile. Although only wounded in the attack, Heydrich died of his injuries on 4 June 1942. His death led to a wave of merciless reprisals by German troops, including the destruction of villages and the killing of civilians.
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Operation Valkyrie was a German World War II emergency plan issued to the Reserve Army to take control in case of civil breakdown. German Army officers General Friedrich Olbricht, Major General Henning von Tresckow, and Colonel Claus von Stauffenberg modified the plan with the intention of using it to take control of German cities, disarm the SS, and arrest the Nazi leadership once Hitler had been assassinated in the July 20 Plot. Hitler’s death (as opposed to his arrest) was required to free German soldiers from their oath of loyalty to him. After lengthy preparation, the plot was carried out in 1944, but failed.
5. Project 404
Project 404 was the code name for a covert United States Air Force advisory mission to Laos during the later years of the Vietnam War. The purpose of Project 404 was to supply the line crew technicians needed to support and train the Royal Laotian Air Force.
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The US government spent over $800 million in order to complete Project Azorian, which involved the recovery of K-129, a Soviet submarine that sank in 1968. The mission was undertaken in 1974 with the hopes of recovering everything on the submarine, which included a nuclear missile, documents, and top secret equipment. The Hugh Glomar Explorer, a mission-specific ship was also created to be used as the primary vessel for the mission.