During this period, the civil war intensified and the economy continued to deteriorate. When prices of basic goods were increased in 1988, riots ensued , and the increase of price was cancelled. Sadiq al mahdi refused to approve a peace plan reached by DUP and the Sudan People's Liberation Army (SPLA) in Nov 1988, the DUP left the Govt.The new govt. consisted only with Umma and the Islamic fundamentalist NIF.
On June 30, 1989, military officers under col. Omar Hasan al-Bashir with NIF instigation and support replaced the Govt. with the evolutionary Command Councilfor National salvation (RCC), a junta composed of 15 military officers assisted by a civilian cabinet.General Al-bashir became president and chief of State, prime minister and and chief of the armed forrces. He continues to hold the exective authority over the Khartoum Govt.
In March 1991, a new penal code , the crminal act of 1991, instituted harsh punishment nationwide, including amputations and stoning. Although the southern states are "officially exempted from these islamic prohibitions and penalties, the 1991 act provides for a possible fture application of Islamic law (shari'a)in the south. In 1993, the trnasferrred all non-muslim judges from the south to the north, replacing them with Muslim judges. The introduction of public order Police to enforce Shari'a law resulted in the arrest and treatment under shari'a law of southerners and other non-muslim living in north.
Nimeiri lived in exile in Egypt from 1985 to 1999, in a village situated in Heliopolis, Cairo. He returned to Sudan in may 1999 to a rupturous welcome that surprised many of his detractors. The next year, he ran in the presidential election against incumbent pressident Omar al-Bashir, but did poorly, obtaining only 9.6% of the votes. From then until his death he was affiliated to the National Congress Party. In 2005,Nimeiri's party the alliance of the People's Working Forces merged with the ruling National Congress Party of Sudan. The National Congress party of Sudan nwgotiated ab end to Sudan's civil war that was signed in a Comprehensive Peace Agreement on jan., 2005.