The National Salvation government sought peace in Sudan from the first day of the June 1989 revolution. Within seven weeks of coming to power, General Omer al-Bashir organised a meeting with the Sudan People's Liberation Movement/Army (SPLM/A), followed in October by a 45-day national dialogue conference – with broad political representation even though there were no political parties – to discuss the root causes and potential solutions of the conflict. The outcome of this conference was the basis for government policy towards the south. In particular, it was agreed that non-Muslims had the right not to be ruled by shari'a just as Muslims had the right to be ruled by shari'a. At that time self-determination was not on the cards.

However, the SPLM/A was not ready to negotiate in 1989. It was in the military ascendancy, having captured much of southern Sudan, and at the same time was struggling to manage the rivalries between the different southern militias and to build its international profile. Government forces responded with a major offensive in the summer of 1992 that recaptured even Torit, the SPLM/A's administrative centre, and forced the SPLM/A back to the negotiating table in Abuja in 1992-93. However, Dr John Garang returned from a visit to the USA in 1993 unwilling to sign this agreement and hostilities worsened. At the same time, Sudan's relationships with neighbours Egypt, Eritrea, Ethiopia and Uganda were tense.

It was in this difficult environment that the 1994 Inter-governmental Authority on Drought and Development (IGADD) Declaration of Principles was presented to the government. It was rejected not because it referred to self-determination but because it was presented as an ultimatum related to the question of Sudan's secularisation and as a precondition to formal talks. Although the government delegation was understandably disappointed that the question of self-determination had been pre-empted by Ali el-Haj's discussions with SPLM-Nasir in Frankfurt in 1992, its real concern was that shari'a should remain a source of law in Sudan, at least among Muslims. For the southerners the question of self-determination was critical, but it was unacceptable to the Government of Sudan (GoS) that this become a precondition for negotiation.

By 1997, both sides were more war-weary, the government had negotiated the Khartoum Peace Agreement with a number of southern militias and was seeking to improve its relations with the other IGAD member states, so the conditions for talks were more conducive. There was also more international pressure, stimulated by increased public awareness of the 'forgotten war.' The government preferred a locally-mediated over an internationally-mediated solution, and had been pursuing a strategy of 'peace from within,' demonstrated by then Vice-President General al-Zubeir's 1995 Political Charter, which paved the way for the Khartoum Peace Agreement in April 1997.

Even then, it was not clear that the SPLM/A was committed to finding a peaceful solution, and between 1997 and 1999 little was achieved. The language remained hostile and both sides kept their cards close to their chest and maintained maximal positions. However, one important factor had changed. The people had tasted peace in the form of increased freedom of movement and economic activity, and they began to put pressure on their leaders not to go back to war.

The really important document in the IGAD process is not so much the Declaration of Principles, which demonstrated little beyond the government's seriousness to engage with the SPLM/A, but the Machakos Protocol of July 2002. Many observers thought that with the signing of the protocol a full agreement was imminent, and in a sense they were right: everything that followed in Naivasha was simply adding detail to the substance that had been agreed in July 2002. The approach of the mediators – by this time General Sumbeiywo had been appointed, and his style was more proactive and military than his predecessor's – was to get agreement paragraph by paragraph and to put every agreed paragraph into a new document that would become the agreement, rather than to try to agree every detail before finalising an agreement. In this way both sides were able to see what progress had been made and what remained to be agreed or further deferred.

Then in September 2002 the SPLA launched an attack on Torit during the talks and the GoS delegation was left with no choice but to abandon negotiations until a ceasefire agreement could be reached. The GoS withdrawal was taken seriously by General Sumbeiywo, and on 15 October 2002 he presented the GoS with a signed agreement for the cessation of hostilities, using the Nuba Mountains Ceasefire Agreement as a model. It is testament to the success of the Machakos Protocol and to the trust that has been built up between both parties since then that this agreement has been consistently renewed and that no shot has been fired by either party.

Much has been made of the personal relationship between Vice-President Ali Osman al-Taha and SPLM/A Chairman Dr John Garang. It is certainly true that the rapport between them was a key factor in finalising the peace agreement; increasingly, the two leaders met together without any form of mediation to discuss and agree the key principles, and without this personal contact the two sides might not have built up the level of trust and cooperation which developed through the period leading up to the Comprehensive Peace Agreement (CPA). But this was not a factor of the road to Machakos, which forms the basis of the CPA: prior to 2002 a number of different statesmen headed the government delegation at different times, including Presidential Peace Advisors Dr Nafie Ali Nafie and Dr Ghazi Salahuddin, Hon Ahmed Ibrahim at-Tahir, former Foreign Minister Mustafa Osman Ismail and Minister Idris Mohamed Abdelgadir. The Machakos Protocol itself was signed by Dr Ghazi Salahuddin and General Salva Kiir Mayardit.

The two sides recognised the importance of their relationship to safeguarding Sudan's post-CPA future. Whether southern Sudan opts to remain within a united Sudan or chooses independence, neighbouring governments must remain friendly. The time and patience given to the process leading to the CPA – in spite of the ups and downs along the way – have proved vital in ensuring that Sudan has friendly relations with its neighbours. But it is not clear that the south is ready for unity yet. A six-year interim period – itself a compromise – is proving a very ambitious timeframe, as is demonstrated by the delays in implementation to date. Establishing the commissions laid down in the CPA requires broad political participation, including from those in the diaspora. It also takes time, and after half a century of war it will take a long time for the south to educate a significant cadre to manage its legislative, judicial, executive and educational institutions. In the meantime, people's expectations of sudden and profound peace dividends have to be managed, and the continuing tribal tensions in the south will need to be resolved, especially between the Dinka who control access to power and the Nuer who control access to oil.

Ultimately Sudan's conflicts are resource-based and fuelled by imbalanced development. President Nimeiri (1969-1985) realised this, and began a programme of decentralisation, but this was under-resourced and too gradual a process to have significant impact on the conflicts. Now that the Fiscal and Financial Allocation Monitoring Committee has oversight, supported by the National Assembly, the devolution programme currently underway will be better funded and hence more effective and more successful.