Some of the dirtiest CIA operations that actually happened 

The Mujahideen

In 1978, Afghanistan became mired in civil war as two Communist parties seized control of the country. When it began to look like anti-Communist rebels were gaining a foothold, the Soviet Union invaded the country to lend support. And that’s when the US, of course, decided to get involved.

The CIA set up camps to train the rebels, known as Mujahideen, in the necessary tactics for beating back the Soviets. Advanced weaponry was also part of the deal, including—importantly—Stinger surface-to-air anti-aircraft missiles. Soviet airstrikes had driven hundreds of guerrillas out of the cities and into the surrounding hills, and mitigating the effectiveness of those strikes proved to be essential in prolonging the conflict, placing a great strain on Soviet resources.

The Soviet Union occupied Afghanistan almost until its collapse in the early 1990s, but the legacy of the Mujahideen lives on. The CIA are finding their own tactics and training turned against them by Mujahideen veterans who have begun their own training programs, producing highly trained and skilled terrorists who now make up the backbone of Al-Qaeda and other radical groups. The US discovered these ramifications the hard way after invading Afghanistan in 2001. The invasion led to a quagmire of an occupation, which—as of this writing—has dragged on for just as long as that of the Soviets.

Source:
https://en.wikipedia.org/wiki/Operation_Cyclone

Operation Mockingbird

Operation Mockingbird was a bit of a two-pronged approach to dealing with the media: on the one hand, journalists were routinely employed by the CIA to develop intelligence and gather information, or to report on certain events in a way that portrayed the US favorably. On the other, there were actual plants within the media—paid off with bribes or even directly employed by the CIA—to feed propaganda to the American public.

Mostly, this program was meant to convince the public of how incredibly scary Communism was, and to make sure that public opinion favored taking out the Red Menace at any expense. Even scarier was the fact that having major newspaper publishers and the heads of TV stations bought and paid for meant that significant overseas events could be excluded from coverage in the media—events like the aforementioned coup in Guatemala, which didn’t see the light of the day in the American press at the time.

Congressional hearings in 1976 (the “Church Committee”) revealed that the CIA had been bribing journalists and editors for years. Following the Church hearings, newly minted CIA director and future President George H.W. Bush announced: “Effective immediately, the CIA will not enter into any paid or contract relationship with any full-time or part-time news correspondent accredited by any U.S. news service, newspaper, periodical, radio or television network or station.” Yet he added that the CIA would continue to welcome unpaid, voluntary support of said journalists.

Sources:
https://en.wikipedia.org/wiki/Operation_Mockingbird

http://www.counterpunch.org/2016/11/30/the-cia-and-the-press-when-the-washington-post-ran-the-cias-propaganda-network/

Operation Mongoose

After the failed Bay of Pigs invasion of Cuba, the Agency’s public image was worse than ever. President Kennedy famously proclaimed that he would “splinter the CIA into a thousand pieces and scatter it to the winds” (shortly before getting shot, but we digress). But to deal with Cuba, he turned to the only person he knew he could trust: his brother, Robert, who organized Operation Mongoose. This operation was conducted by the Department of Defense in conjunction with the CIA, under Robert Kennedy’s supervision. He told his team at its first briefing that deposing Castro was “the top priority of the US government—all else is secondary—no time, money, effort, or manpower is to be spared.”

Among the dozens of extremely silly methods of assassination proposed: infecting Castro’s scuba gear with tuberculosis; planting exploding seashells at a favorite diving site; slipping him a poisoned fountain pen; and even even poisoning or slipping a bomb into one of his cigars. Castro’s bodyguard asserted that there were hundreds of CIA schemes on Castro’s life—and they all ended in failure, a gigantic waste of time and money. Castro was Cuba’s dictator for forty-nine years, stepping down in 2008 due to failing health, and appointing his younger brother as his replacement.

Source:
https://en.wikipedia.org/wiki/Cuban_Project

Fake Pakistani Vaccine Drive

The May 2011 raid that killed Osama Bin Laden was the result of an insane amount of intelligence collecting and planning; regardless of his crimes, conducting a US military operation to kill a foreign national on Pakistani soil was bound to have myriad consequences. A courier had been tracked to an Abbottabad compound, where it was pretty damn certain Bin Laden was hiding. But before conducting the raid, they had to be absolutely sure—and one method of collecting this proof was shady in the extreme.

The CIA recruited a respected Pakistani doctor to organize a fake vaccination drive in the town, and in the process collected thousands of blood samples from children in the area children—among them, as it turned out, Bin Laden’s children. Since theirs was a fairly upscale section of town, the campaign began in a poorer area to make it look more authentic, then moved on to the neighborhood housing the Bin Laden compound a month later—without even following up with the required second or third doses in the poor area. The whole thing worked—with consequences.

For one thing, Dr. Shakil Afridi—the doctor involved—has been convicted of treason by the Pakistani government and given a thirty-three-year prison sentence (“Wouldn’t any country detain people for working for a foreign spy service?” one Iranian official helpfully pointed out). For another, the campaign has caused irreparable damage to organizations that carry out legitimate vaccinations. There are deep-seated suspicions in many Middle Eastern regions about those who provide vaccinations, and this gambit to assist in finding Bin Laden has only bolstered those suspicions—particularly in Nigeria, India and of course Pakistan, where efforts to eradicate polio are ongoing.

Source:
https://en.wikipedia.org/wiki/Shakil_Afridi

The Phoenix Program

Phoenix was a program headed by the CIA, in conjunction with US Special Forces and Australian and South Vietnamese commandos, during the Vietnam War. Its purpose was simple: assassination. And although this was a military unit, their targets weren’t military, but civilian.

From 1965 to 1972, Phoenix was involved in the kidnapping, torture, and murder of thousands upon thousands of citizens. People deemed critical to the infrastructure of the Viet Cong, or thought to have knowledge of VC activities, were rounded up and taken to regional interrogation centers, were they were subjected to: “rape, gang rape, rape using eels, snakes, or hard objects, and rape followed by murder; electric shock . . . rendered by attaching wires to the genitals or other sensitive parts of the body, like the tongue; the ‘water treatment’; the ‘airplane’ in which the prisoner’s arms were tied behind the back, and the rope looped over a hook on the ceiling, suspending the prisoner in midair, after which he or she was beaten; beatings with rubber hoses and whips; the use of police dogs to maul prisoners…”

Phoenix was the subject of 1971 Congressional hearings on abuse. Former members described it as a “sterile depersonalized murder program”, and it was phased out after negative publicity, though the replacement program F-6 was quietly phased in to take its place.

Sources:
https://en.wikipedia.org/wiki/Phoenix_Program

http://www.thepeopleshistory.net/2014/07/phoenix-program-cia-terrorism-campaign.html