In the mid-1990s a-Bashir and al-Turabi began to differ with each other due to the different attitude towards the Islamic fundamentalists by both of them. Al-Turabi had a close link with the Islamic Fundamentalist.
After the incident of 9/11 in 1991, in New York, the United states had listed Sudan as a state sponsor of terrorism since 1993, mostly due to Al-Bashir and Al-Turabi taking complte power in the early 1990s.US firms have been barred from doing any business in udan since 1997. In 1998, the al-Shifa pharmaceutical factory in Khartoum was destroyed by a US cruise missile strike because of its alleged production of chemical weaapons and links to al-Qaeda, . However the US state department Bureau of intellligence and research wrote a report in 1999 questioning the attack on the factory, suggesting that the connection to bin laden was not accurate ; James Risen reported in the New York Times : "now the analysis renewed their doubts and told assistant secretary of state Phillis Oakley that the CIA's evidence on which the attack was based was inadequate. Later it was found that the case of association of bin Laden and chemical weapons were weak.
On 14 July, 2008, the Chief Prosecutor of the International Criminal Court (ICC) Luis Moreno-Ocampo, alleged that al-Bashir bore individual criminal responsibility for genocide, crimes against humanity and war crimes committed since 2003 in Darfur.
The arrest warant is supported by NATO, the Genocide Intervention network and Amnesty international.
Ultimately the charges were rejected and he was not arrested.