The most powerful leader of the new government was the secretary general of the Iraqi Ba'ath Party, Ali Salih al-Sa'di, who controlled the National Guard militia and organized a massacre of hundreds—if not thousands—of suspected communists and other dissidents following the coup.

[7] The government lasted approximately nine months, until Arif disarmed the National Guard in the November 1963 Iraqi coup d'état, which was followed by a purge of Ba'ath Party members.

Gradually, Abd al-Karim Qasim's relations with some of his fellow members of Al-Ahrar worsened, and his relationship with the unionist and nationalist currents, which had played an active role in supporting the 1958 movement, became strained.

The coup began in the early morning of 8 February 1963, when the communist air force chief, Jalal al-Awqati, was assassinated, and tank units occupied the Abu Ghraib radio station.

To counter that sentiment and to terrorize his supporters, Qasim's dead body was displayed on television in a five-minute propaganda video, The End of the Criminals, which included close-up views of his bullet wounds amid disrespectful treatment of his corpse, which is spat on in the final scene.

However, the secretary general of the Ba'ath Party, Ali Salih al-Sa'di, used his control of the National Guard militia, commanded by Mundhir al-Wanadawi, to establish himself as the de facto new leader of Iraq and had more authority in reality than al-Bakr or Arif.

The nine-month rule of al-Sa'di and his civilian branch of the Ba'ath Party has been described as "a reign of terror" as the National Guard, under orders from the Revolutionary Command Council (RCC) "to annihilate anyone who disturbs the peace," detained, tortured, or executed thousands of suspected Qasim loyalists.

Furthermore, the National Guard, which developed from a core group of perhaps 5,000 civilian Ba'athist partisans but increased to 34,000 members by August 1963, who were identified by their green armbands, was poorly disciplined, as militiamen engaged in extensive infighting and created a widespread perception of chaos and disorder.

[14] Pertinent contemporary documents relating to the CIA's operations in Iraq have remained classified[15][16] and as of 2021, "[s]cholars are only beginning to uncover the extent to which the United States was involved in organizing the coup,"[17] but are "divided in their interpretations of American foreign policy.

[3][18][23] Eric Jacobsen, citing the testimony of contemporary prominent Ba'athists and U.S. government officials, states that "[t]here is ample evidence that the CIA not only had contacts with the Iraqi Ba'th in the early sixties, but also assisted in the planning of the coup.

"[24] Nathan J. Citino writes that "Washington backed the movement by military officers linked to the pan-Arab Ba‘th Party that overthrew Qasim," but that "the extent of U.S. responsibility cannot be fully established on the basis of available documents," and that "[a]lthough the United States did not initiate the 14 Ramadan coup, at best it condoned and at worst it contributed to the violence that followed.

"[26] Ammash was described as "Western-oriented, anti-British, and anti-Communist," and known to be "friendly to the service attaches of the US Embassy in Baghdad," while future U.S. ambassador to Iraq, Robert C. Strong, would refer to Jawad as "one of our boys.

"[24] Former U.S. ambassador to Saudi Arabia, James E. Akins, who worked in the Baghdad Embassy's political section from 1961 to 1964, would state that he personally witnessed contacts between Ba'ath Party members and CIA officials,[24] and that:The [1963 Ba'athist] revolution was of course supported by the U.S. in money and equipment as well.

"[6] On the other hand, Wolfe-Hunnicutt, citing contemporary U.S. counterinsurgency doctrine, notes that assertions of CIA involvement in the Ba'athist purge campaign "would be consistent with American special warfare doctrine" regarding U.S. covert support to anti-communist "Hunter-Killer" teams "seeking the violent overthrow of a communist dominated and supported government,"[39] and "speaks to a larger pattern in American foreign policy," drawing parallels to other instances where the CIA compiled lists of suspected communists targeted for execution, such as Guatemala in 1954 and Indonesia in 1965-66.

"[36] Lakeland, a former SCI participant, "personally maintained contact following the coup with a National Guard interrogator," and may have been influenced by his prior interaction with then-Major Hasan Mustafa al-Naqib, the Iraqi military attaché in the U.S. who defected to the Ba'ath Party after Qasim "upheld Mahdawi's death sentences" against nationalists involved in the 1959 Mosul uprising.

[45] The Kennedy administration officially advocated a diplomatic settlement to the First Iraqi–Kurdish War, but its provision of military aid to the Ba'athist government emboldened Iraqi hardliners to resume hostilities against Kurdish rebels on June 10, after which Iraq requested additional emergency U.S. assistance including napalm weapons.

President Kennedy approved the arms sale in part on the recommendation of senior adviser Robert Komer and the weapons were provided, but an offer by Iraqi general Hasan Sabri al-Bayati to reciprocate this gesture by sending a Soviet T-54 tank in Iraq's possession to the U.S. embassy in Baghdad for inspection became something of a "scandal" as Bayati's offer had not been approved by al-Bakr, Foreign Minister Talib El-Shibib, or other senior Iraqi officials.

"[49] Marion Farouk-Sluglett and Peter Sluglett describe the Ba'athists as having cultivated a "profoundly unsavory image" by "acts of wanton brutality" on a scale without prior precedent in Iraq, including "some of the most terrible scenes of violence hitherto experienced in the postwar Middle East."

"[50] Batatu recounts: In the cellars of al-Nihayyah Palace, which the [National Guard's] Bureau [of Special Investigation] used as its headquarters, were found all sorts of loathsome instruments of torture, including electric wires with pincers, pointed iron stakes on which prisoners were made to sit, and a machine which still bore traces of chopped-off fingers.