In the late 1980s, Hissène Habré became worried about possible rivals and began an increasingly repressive period of arbitrary arrests and executions. He created a security force consisting solely of members of his own ethnic group and equipping them better than the forces of which Déby and his cousin were in charge. The favoritism towards this force provoked a rebellion of the regular forces. Déby and his cousin were warned that their lives were in danger and fled the capital.
Déby made his way to the Sudan, where he formed the Patriotic Movement of Salvation (MPS) and began a reconquest of Chad. Déby's mission was completed by December 1990, having obtained military equipment from Libya, his former enemy. The French acquiesced to his designs by withholding support and information on Déby's troop movements and location from Habré. Habré fled the capital, allegedly with carloads of stolen funds, and Déby took charge of the country.
Though Déby declared his intention of moving toward a democratic government, the process moved slowly. Political parties were recognized in 1991, and a national conference to work out the transition began in January 1993. It concluded its work with a transitional charter and prime minister elected by the delegates. Déby was to remain as president and chief of the armed forces during the transition period. This period was expected to last one year, with the possibility of a one-year extension. In 1995, Déby finally set up a national independent commission. A draft Constitution was ready for referendum vote in March 1996. The new Constitution, which was approved by the voters in a 71% turnout, set up a president elected by universal suffrage for a five-year term with eligibility for reelection to one more five-year term.
During the election campaign, Déby was careful to travel to all regions of the country and even to apologize to the electorate in some areas that had experienced harsh treatment from his troops. He was the designated candidate of the MPS, which had been reformed into a political party. But he campaigned as the Republic Front candidate, a coalition made up of 12 political parties. Fifteen candidates were eventually accepted for the official list, including many of the major political and military figures and representing a wide range of viewpoints. The turnout in the first round of voting was 69%. The second round achieved a 77% turnout, with Déby garnering 69% of the votes. The legislative elections that followed in January and February 1997 brought Déby's MPS an absolute majority of 63 of the 125 assembly seats, with nine other parties sharing the remaining 62 seats.
In the controversial May 2001 presidential elections, the Constitutional Council denied the opposition's appeal to annul the elections, and on June 13 declared Déby the winner with 63.17% of the votes, followed by Yorongar with 16.35%, and Kebzabo and Kamougué with 7% and 6.02% respectively. The Council reported a voter turn-out of 61.4%. Alleging fraud, malpractice and irregularities in vote counting, six of the defeated candidates called for a boycott of the next legislative elections.