The negotiations and accords until 1988 had all been bilateral, either between Angola and the US, Angola and South Africa or the US and South Africa. Luanda refused any direct contact with UNITA, instead looking for direct talks with Savimbi's sponsors in Pretoria and Washington. The negotiations usually took place in third countries and were mediated by third countries. The US, although clandestinely supporting the UNITA,often acted as a mediator itself. From 1986, the Soviet Union expressed its interest in a political solution. It was increasingly included in consultations but never directly involved in the negotiations. Endeavours for a settlement had intensified after the fighting in southern Angola broke out in 1987. It was agreed, that this time only governments were to take part in the negotiations, which excluded participation by UNITA.
From the start of the negotiations in 1981, the Cubans had not asked and were not asked to participate and the Americans did not have in mind to include them. Castro signalled interest to the US in July 1987 while preparations for the FAPLA offensive against UNITA were under way. He let the Americans know that negotiations including the Cubans would be much more promising. But it was not until January 1988 that US secretary of state George Schultz authorized the American delegation to hold direct talks with the Cubans with the strict provision that they only discuss matters of Angola and Namibia but not the US-embargo against Cuba. The Cuban government joined negotiations on 28 January 1988. They conceded that their withdrawal had to include all troops in Angola including the 5,000 they had in mind to keep in the north and in Cabinda for protection of the oil fields. Yet, US support for UNITA was going to be continued and was not to be an issue at the discussions.
The US continued its two-track policy, mediating between Luanda and Pretoria as well as providing aid to UNITA through Kamina airbase in Zaire. The Reagan administration's first priority was to get the Cubans out of Angola. In its terminology, by supporting UNITA the US was conducting "low-intensity-warfare". According to a western diplomat in Luanda, the US "first wanted to get the Cubans out and afterwards wanted to ask the South Africans to kindly retreat from Namibia". David Albright reported that South African officials believe that Armscor's preparations for a nuclear test at Vastrap were discovered by Soviet or Western intelligence agencies, and that this discovery led to increased pressure on Cuba and the Soviet Union to withdraw from Angola.
Crocker had initially been unable to convince anyone in Europe of his linkage concept, which tied Namibian independence to Cuban withdrawal. On the contrary, the European Union was ready to help with Angolan reconstruction.
Pretoria had walked out of the negotiations two years before and it was necessary to get South Africa back to the table. On 16 March 1988, the South African Business Day reported that Pretoria was "offering to withdraw into Namibia -- not from Namibia -- in return for the withdrawal of Cuban forces from Angola. The implication is that South Africa has no real intention of giving up the territory any time soon." After much coaxing the South African government joined negotiations in Cairo on 3 May 1988 expecting Resolution 435 to be modified. Defence Minister Malan and President P.W. Botha asserted that South Africa would withdraw from Angola only "if Russia and its proxies did the same." They did not mention withdrawing from Namibia.
In July 1987, Cuba and Angola had offered to speed up Cuban withdrawal. 20,000 troops stationed south of the 13th parallel could be sent home within two instead of three years on the condition that the SADF retreated from Angola, that US and South African support for UNITA was terminated, that Angola's sovereignty was respected and UN Resolution 435 was implemented. Botha flatly rejected any move before the Cubans withdrew from Angola. In order to "torpedo" the initiatives, Malan "innocently" suggested direct negotiations with Moscow so that the Angola conflict could be solved after the example of Afghanistan. The Kremlin responded mockingly that Angola and Afghanistan hardly had more in common than the initial letters in their name. Thus, the timeframe of withdrawal remained the biggest obstacle for a settlement. Chester Crocker proposed a tighter timeframe of total withdrawal within three years which the Angolans rejected.
It was only after the battle at Cuito Cuanavale that the Botha government showed a real interest in peace negotiations. The Cuban military strategy in southern Angola in 1988 brought urgency to the negotiations. After stopping the SADF counter offensive at Cuito Cuanavale and opening a second front to the west, the Cubans in Angola had raised the stakes and reversed the situation on the ground. In fact, the US wondered whether the Cubans would stop their advance at the Namibian border. The heavy loss of life at Calueque sparked outrage in South Africa and it ordered an immediate retrenchment. The SADF forces remaining in eastern Angola were instructed to avoid further casualties. After the bloody clashes on 27 June, the SADF on 13 July set up 10 Division in defence of northern Namibia, in case the Cubans attempted an invasion. Thus, Jorge Risquet, head of the Cuban delegation, responded to South African demands: "The time for your military adventures, for the acts of aggression that you have pursued with impunity, for your massacres of refugees ... is over… South Africa is acting as though it was a victorious army, rather than what it really is: a defeated aggressor that is withdrawing ... South Africa must face the fact that it will not obtain at the negotiating table what it could not achieve on the battlefield." Crocker cabled Secretary of State George Shultz that the talks had taken place "against the backdrop of increasing military tension surrounding the large build-up of heavily armed Cuban troops in south-west Angola in close proximity to the Namibian border ... The Cuban build-up in southwest Angola has created an unpredictable military dynamic."
The Cubans were the driving force behind the negotiations in the final phase beginning in July 1988. The Angolan allies, first wanting to maintain the status quo after the successes in the south, had to be persuaded to continue. Worried that the fighting in Cunene escalated into an all-out war, Crocker achieved a first breakthrough in New York on 13 July. The Cubans replaced Jorge Risquet by more conciliate Carlos Aldana Escalante and agreed in general to withdraw from Angola in turn for Namibian independence. Cuba's calculations were simple: Once the South Africans were out of Namibia and Resolution 435 was implemented, Pretoria would be without a safe base to operate from and to destabilize Angola. The Luanda government could hold off UNITA without Cuban help. Cuba also figured that SWAPO, their regional ally, would pipe the tune in Namibia.
In the "New York Principles" the parties agreed to settle their differences through negotiations. The following round of talks in Cape Verde, 22–23 July 1988, only produced a commitment to set up a Joint Monitoring Commission which was to oversee the withdrawals. On 5 August, the three parties signed the "Geneva Protocol" laying out South African withdrawal from Angola starting 10 August and to be completed 1 September. By then Cubans and Angolans were to agree on Cuban troop withdrawal. On 10 September a tripartite peace settlement was to be signed and Resolution 435 was to be implemented on 1 November. A ceasefire came into effect on 8 August 1988. Pretoria pulled its remaining forces out of Angola by 30 August 1988. Cuban and SWAPO forces moved away from the southern border. By then, a formula for the Cuban withdrawal from Angola had not been found as there was still a gap of 41 months between the Cuban and South African proposal and it took another five rounds of talks between August and October 1988 to find a settlement. The negotiations were interrupted to await the outcome of the US elections in which George H. W. Bush succeeded Ronald Reagan on 8 November 1988. In the meantime, a FAPLA offensive was under way and UNITA was close to collapse threatening another South African intervention and putting Cuban forces in Angola on alert. Yet, Pretoria did not have in mind to endanger the talks and refrained from interference.
It was only after the US elections that the parties agreed on a timetable for the Cubans. On 22 December 1988, one month before Reagan's second term ended, Angola, Cuba and South Africa signed the Three Powers Accord in New York, arranging for the withdrawal of South African troops from Angola and Namibia, the independence of Namibia and the withdrawal of Cuban troops from Angola. Cuba agreed to an overall time frame of 30 months and to withdraw within 27 months after implementation of Resolution 435. The timetable agreed upon provided for the following steps:
· until 1 April 1989: withdrawal of 3,000 Cuban troops (3 months)
· 1 April 1989: Implementation of Resolution 435 and start of 27-month time frame for total withdrawal
· 1 August 1989: all Cuban troops moved north of 15th parallel (7 months)
· 31 October 1989: all Cuban troops moved north of 13th parallel (10 months)
· 1 November 1989: free elections in Namibia and 50% of all Cuban troops withdrawn from Angola
· 1 April 1990: 66% of all Cuban troops withdrawn (15 months)
· 1 October 1990: 76% of all Cuban troops withdrawn (21 months)
· 1 July 1991: Cuban withdrawal completed (30 months)
The accord ended 13 years of Cuban military presence in Angola which was finalized one month early on 25 May 1991. At the same time the Cubans removed their troops from Pointe Noire (Republic of the Congo) and Ethiopia.