In Summary
President Salva Kiir and rebel leader Dr Riek Machar have declared a ceasefire beginning midnight of August 29. This was one of the requirement of the agreement where both parties were to declare a ceasefire within 72 hours of the signing.
For Dr Machar however his breakaway generals have vowed to continue fighting both the government and the rebels on the grounds that he was simply looking for government positions.
One of those opposed to the deal, Chief of General Staff Paul Malong, tried unsuccessfully to persuade some of the members of the Cabinet to reject the deal during Monday's expanded leadership meeting involving state governors, and members of the allied political parties inside and outside the government.
During the signing on Wednesday evening, Gen Malong was confined in his house in Juba, reportedly under house arrest, while Information Minister Michael Makuei reportedly walked out when President Kiir was about to sign the document.
Dr Cirino Hiteng, one of the former detainees, told The EastAfrican that there is no political will in Juba, beginning with the reluctance to sign the agreement in Addis Ababa on August 17. The other challenge, he says, is meeting deadlines as per the agreement, for example, convening a workshop on security and the establishment of a unified command.
"President Kiir's supporters dread the idea of Dr Machar coming back to the government and displacing Vice President James Wani Igga, for the second time. The other major issue is the integration of two armies. Forming a unified army that's not tribally based will not be easy," said Kiur Garang, an author based in Camada.
On the rebel side, Gene Peter Gatdet Yaak, who was dropped from his post of director for operations in the rebel movement, is opposed to the deal and remains holed up in Khartoum, raising fears that he could mobilise his forces to undermine the implementation of the peace deal.
The existing Igad Monitoring and Verification Mechanism will transform itself into the Ceasefire and Transitional Security Arrangements Monitoring Mechanism and will report on the progress of the Permanent Ceasefire and Transitional Security Arrangements (PCTSA).
It will monitor compliance and report directly to the Joint Monitoring and Evaluation Commission on the implementation of the PCTSA during the transition period.
One of the key concerns to the government was that the US started circulating a document on sanctions at the United Nations even before the expiry of the 15-day grace period that was given by the Inter-Governmental Authority on Development (Igad), thereby intimidating the government into signing the document.
South Sudan deputy ambassador to Kenya, James Morgan argued that the Troika -- US, UK and Norway -- have been pushing a peace agreement that favours their interests and not the welfare of the people of South Sudan.
"Our mediation team in Addis Ababa did not do well because any objection from them was overruled by Igad mediators. We are not against peace but an imposed deal will not silence the guns, especially from the rebel side," said Mr Morgan.
At the signing ceremony on Wednesday, President Kiir sought to attach a 12-page list of reservations on many key points of the deal. But White House spokesman Josh Earnes warned that it does not recognise the list.
One of the major challenges of the implementation will be the disarmament, demobilisation and reintegration because the government maintains that only the Sudanese People's Liberation Army (SPLA) that defected with Dr Machar will be integrated into the national army within 18 months while the rebels want the militia known as the White Army to be integrated as well.
Adel Sandrai, Dr Machar's representative in Kenya, said that the rebel movement will not demobilise their soldiers during the 90 days pre-transition period because they need them to be integrated into the national army.
Dr Machar will serve as the commander-in-chief of the opposition forces in the first 90 days after signing until the armies of Kiir and Dr Machar are unified.
After that he will be acting commander in chief of the national defence forces only in the absence of the president.
The Transitional Government of National Unity is expected to be in place by December 1 to govern for 30 months. It also means the Transitional Constitution of South Sudan 2011 would no longer be valid during the implementation period and will be replaced by the permanent Constitution of South Sudan to be put in place by the transitional government.
Sarah Jackson, Amnesty International's Deputy Regional Director for East Africa, the Horn and the Great Lakes said that the international community must remain vigilant and the UN Security Council, the African Union and South Sudan's neighbours must ensure that mechanisms established during the peace process are successfully implemented, which could also help bring the perpetrators of war crimes to justice.