'Operation Cyclone' was one of the longest and most expensive covert CIA operations ever undertaken. Funding began with $20–30 million per year in 1980 and rose to $630 million per year in 1987. CIA financial aid to the insurgents within Afghanistan was approved in July of 1979, six months before the Soviet invasion, though after the Soviets were already covertly engaged there. Arms were sent to CIA-loyal Afghani rebels only after the formal Soviet invasion.

The Soviet War in Afghanistan was a nine-year conflict involving the Soviet Union, supporting the Marxist-Leninist government of the Democratic Republic of Afghanistan against the indigenous Afghan Mujahideen and foreign 'Arab–Afghan' volunteers. The mujahideen found military and financial support from a variety of sources including the United States, Saudi Arabia, the United Kingdom, Pakistan, Egypt, China and other nations. The Afghan war became a proxy war in the broader context of the late Cold War. On April 14, 1979, the Afghan government requested that the USSR send 15 to 20 helicopters with their crews to Afghanistan, and on June 16, the Soviet government responded and sent a detachment of tanks, BMPs, and crews to guard the government in Kabul and to secure the Bagram and Shindand airfields. In response to this request, an airborne battalion, commanded by Lieutenant Colonel A. Lomakin, arrived at Bagram Air Base on July 7. They arrived without their combat gear, disguised as technical specialists. They were the personal bodyguards for President Taraki. The paratroopers were directly subordinate to the senior Soviet military advisor and did not interfere in Afghan politics. On July 3, 1979, Carter signed a presidential finding authorizing funding for anticommunist guerrillas in Afghanistan as a part of the Central Intelligence Agency program called Operation Cyclone, led by their elite Special Activities Division, which would later include the massive arming of Afghanistan's mujahideen.

The initial Soviet deployment of the 40th Army in Afghanistan began on December 24, 1979 under Soviet premier Leonid Brezhnev. The final troop withdrawal started on May 15, 1988, and ended on February 15, 1989 under the last Soviet leader Mikhail Gorbachev. Due to the interminable nature of the war, the conflict in Afghanistan has sometimes been referred to as the Soviet Union's 'Vietnam War.'

President Jimmy Carter insisted that what he termed 'Soviet aggression' could not be viewed as an isolated event of limited geographical importance but had to be contested as a potential threat to US influence in the Persian Gulf region. The US was also worried about the USSR gaining access to the Indian Ocean by coming to an arrangement with Pakistan.

On July 3, 1979, Carter signed the first directive for secret aid to the opponents of the pro-Soviet regime in Kabul. The aim of US was to drag the Soviet Union into what then US Secretary of State Zbigniew Brzezinski liked to call the 'Afghan trap.'

The Afghans were supported by a number of other countries, with the US and Saudi Arabia offering the greatest financial support.

The United States began training insurgents in, and directing propaganda broadcasts into Afghanistan from Pakistan in 1978. Then, in early 1979, U.S. foreign service officers began meeting insurgent leaders to determine their needs. After the Soviet deployment, Pakistan's military ruler General Muhammad Zia-ul-Haq started accepting financial aid from Western powers to aid the Mujahideen. (They are now called 'The Taliban.' - Rob, editor.) In 1981, following the election of US President Ronald Reagan, aid for the Mujahideen through Zia's Pakistan significantly increased, mostly due to the efforts of Texas Congressman Charlie Wilson and CIA officer Gust Avrakotos.

US 'Paramilitary Officers' from the CIA's Special Activities Division (U.S. Army Delta Force - Rob, editor.) were instrumental in training, equipping and sometimes leading Mujihadeen forces against the Soviet Army. Although the CIA in general and Charlie Wilson, a Texas Congressman, have received most of the attention, the key architect of this strategy was Michael G. Vickers, a young Paramilitary Officer. Michael Pillsbury, a senior Pentagon official overcame bureaucratic resisistance during 1985-1986, and persuaded President Reagan to provide hundreds of Stinger missiles to the Mujihadeen forces against the Soviet Army.

Between December 25, 1979 and February 15, 1989, a total of 620,000 soldiers served with the forces in Afghanistan (though there were only 80,000-104,000 serving at one time): 525,000 in the Army, 90,000 with border troops and other KGB sub-units, 5,000 in independent formations of MVD Internal Troops, and police forces. A further 21,000 personnel were with the Soviet troop contingent over the same period doing various white collar and blue collar jobs.

The total irrecoverable personnel losses of the Soviet Armed Forces, frontier, and internal security troops came to 14,453. Soviet Army formations, units, and HQ elements lost 13,833, KGB sub-units lost 572, MVD formations lost 28, and other ministries and departments lost 20 men. During this period 417 servicemen were missing in action or taken prisoner; 119 of these were later freed, of whom 97 returned to the USSR and 22 went to other countries. The rest were murdered by their captors.

Osama Bin Laden recruited 4,000 volunteers from his own country and developed close relations with the most radical Mujahideen leaders. He also worked closely with the CIA. Since September 11, 2001, CIA officials have been claiming they had no direct link to bin Laden. Education in Afghanistan in the years preceding the Soviet-Afghan war was largely secular. The US covert education destroyed secular education. The number of CIA sponsored religious schools (madrasahs) increased from 2,500 in 1980 to over 39,000. From the outset of the Soviet Afghan war in 1979, Pakistan under military rule actively supported the Islamic brigades. In close liaison with the CIA, Pakistan's military intelligence, the Inter-Services Intelligence (ISI), became a powerful organization, a parallel government, wielding tremendous power and influence.

The ISI had a staff composed of military and intelligence officers, bureaucrats, undercover agents and informers, estimated at 150,000. Meanwhile, CIA operations had also reinforced the Pakistani military regime led by General Zia Ul Haq.

Relations between the CIA and the ISI had grown increasingly warm following [General] Zia's ouster of Bhutto and the advent of the military regime. During most of the Afghan war, Pakistan was more aggressively anti-Soviet than even the United States. Soon after the Soviet military invaded Afghanistan in 1980, Zia [ul Haq] sent his ISI chief to destabilize the Soviet Central Asian states. The CIA only agreed to this plan in October of 1984.

The ISI operating virtually as an affiliate of the CIA, played a central role in channeling support to Islamic paramilitary groups in Afghanistan and subsequently in the Muslim republics of the former Soviet Union.

Acting on behalf of the CIA, the ISI was also involved in the recruitment and training of the Mujahideen. In the ten year period from 1982 to 1992, some 35,000 Muslims from 43 Islamic countries were recruited to fight in the Afghan jihad.

The madrassasin Pakistan, financed by Saudi charities, were also set up with US support with a view to 'inculcating Islamic values.' The camps became virtual universities for future Islamic radicalism. Guerilla training under CIA-ISI auspices included targeted assassinations and car bomb attacks.

Weapons' shipments were sent by the Pakistani army and the ISI to rebel camps in the North West Frontier Province near the Afghanistan border. The military governor of the province was Lieutenant General Fazle Haq, who allowed hundreds of heroin refineries to set up in his province. Harvested gum opium was trucked to a Pakistani Army base and taken over by CIA personnel where it was trans-shipped to Columbia by CIA proprietary aircraft companies.

Beginning around 1982, Pakistani army trucks carrying CIA weapons from Karachi often picked up heroin in Haq’s province and return loaded with heroin. They were protected from police search by ISI papers. During the Reagan administration, Osama, who belonged to the wealthy Saudi Bin Laden family, was put in charge of raising money for the Islamic brigades. Numerous charities and foundations were created.

The operation was coordinated by Saudi intelligence, headed by Prince Turki al-Faisal, in close liaison with the CIA. The money derived from the various charities were used to finance the recruitment of Mujahadien volunteers.

Al Qaeda, 'The Base' in Arabic, was a CIA-instituted and maintained data bank of volunteers who had enlisted to fight in the Afghan jihad. That data base was initially also controlled by Osama bin Laden. U.S. CIA and U.S. Army counterinsurgency experts worked closely with the Pakistan's Inter-Services Intelligence (ISI) in organizing Mujahideen groups and in planning operations inside Afghanistan. But the most important contribution of the U.S. was to bring in men and material from around the Arab world and beyond. The most hardened and ideologically dedicated men were sought on the logic that they would be the best fighters. Advertisements, paid for from CIA funds, were placed in newspapers and newsletters around the world offering inducements and motivations to join the Jihad.