Ibrahim served as the state minister for education in Darfur between 1991 and 1994 in
al-Fashir,
North Darfur. A physician, Ibrahim spent four months in 1992 to fight
Sudan People's Armed Forces. By Ibrahim's own account, he was disaffected with the Islamist movement by 2000 after seeing the economic neglect of the NIF, as well as its support to armed militias. At this time, he became part of a
covert cell of Islamists who were seeking to change the NIF from inside. Ibrahim went on to serve as the state minister for social affairs in
Blue Nile in 1997 before a post as adviser to the governor of
Southern Sudan in
Juba in 1998. However, others noted that he never received a national level appointment. Ibrahim's colleague in JEM, Ahmad Tugod, stated, "Khalil is not a first or even second class political leader. [...] He struggled all of his life to get a post in
Khartoum." He quit the post in August 1998, several months before the end of his appointment, and formed an NGO called "Fighting Poverty". In December 1999, when al-Bashir sidelined al-Turabi with the help of
Ali Osman Taha, Ibrahim was in the
Netherlands, studying for a master's degree in public health at
Universiteit Maastricht. In the meantime, the structure of covert cells that Ibrahim had helped set up in 1994 had spread to Khartoum. The dissidents, dubbing themselves "The Seekers of Truth and Justice" published the
Black Book in 2000, claiming Riverine Arabs dominated political power and resources. In 2001, Ibrahim was one of twenty people sent out of the country by the dissidents to go public. In August 2001, Ibrahim published a press release from the
Netherlands, in which he announced the formation of the
Justice and Equality Movement. The JEM has a relatively small ethnic base of support, limited to the Kobe Zaghawa, including many kinsmen from across the Chadian border. ==Darfur conflict==