As a colonial legislator, Tombalbaye had managed to create a coalition of progressive forces from both the north and south of the country, isolating the more conservative Muslim factions in the center. It was hoped that he would continue to do this after independence, while creating the economic and political infrastructure in the vast, underdeveloped country of vastly disparate ethnic and religious groups. Instead he adopted an autocratic form of government, eliminating opposition within his party, banning other parties, and in 1963, responding to rioting by dissolving the National assembly. At the same time, he began nationalizing the civil service, replacing French administrators with locals, who were generally less competent in their new positions. To fund the process, he imposed a "National Loan" on the population, which perceived it only as a sharp increase in taxes.
Perhaps the greatest criticism of his Africanization program was that it failed to account for the large population in the north and center of the country, who were Muslim Gorane and did not identify with the African south. A series of incidents convinced this population that their fate under Tombalbaye would be no better than it was under France: colonial rule had simply shifted to the south. On November 1, 1965 riots in the Guéra Prefecture led to five hundred deaths. This sparked a series of disturbances throughout the north and center of the country, compounded by involvement by Chad's neighbors, Libya to the north and Sudan to the east. The most prominent movement in this period was the National Liberation Front of Chad, based in Sudan, but it, like all other movements in the region, was plagued by rivalry and division. Nevertheless, Tombalbaye's government was unable to defeat the rebels, forcing him to resort to calling on the former colonial power, France, for assistance, citing treaties the two countries had signed at independence.
France agreed to enter the fray, provided that Tombalbaye initiate a series of reforms to the army, government, and civil service. Taxes and laws imposed arbitrarily by Tombalbaye were to be rescinded, and the country's traditional sultans had their role as tax collectors restored (for which they received 10 percent of the income). He agreed to this in 1969 and the country embarked on a gradual liberalization process. In elections in 1969, several hundred political prisoners were released from prison, but Tombalbaye was still the only candidate on the ballot.
A further sign of liberalization came in 1971, when Tombalbaye admitted to the Congress of the PPT that he had made mistakes. Steps were taken to reform the government, and more Gorane were included in his new government. Order seemed to have been restored, and France withdrew its troops from the country.
Progress came to a grinding halt in August, 1971, when an attempted coup with links to Libyan leader Mu'ammar al-Qadhafi was uncovered. Tombalbaye immediately severed relations with his northern neighbor and even allowed anti-Qadhafi forces to operate from his territory. In return, Qadhafi granted formal recognition and aid to what remained of the FROLINAT opposition to Tombalbaye. Meanwhile, in the south, where Tombalbaye had his greatest support, he responded to a strike by students by replacing the popular Chief of Staff Jacques Doumro with Colonel Félix Malloum. The country was in the grip of a crippling drought, and Tombalbaye rescinded his amnesty to political prisoners. By the end of 1972, over 1,000 political prisoners had been arrested. At the same time, he also made overtures to the Arab world, reducing Libyan support for FROLINAT and fomenting infighting in that organization.
Nevertheless, Tombalbaye was feeling insecure with his own government as well. In a bizarre twist of events, he arrested major PPT leaders, including Félix Malloum, for allegedly using magic to overthrow him in what was known as the "Black Sheep Plot," for the animals they allegedly sacrificed. In August, Tombalbaye disbanded the PPT and replaced it with the National Movement for Social and Cultural Revolution (MNRCS). Under the guise of authenticité, the new movement promoted Africanization: the capital of Fort-Lamy was renamed N'Djamena and Tombalbaye himself changed his given name from François to Ngarta. Christianity was disparaged, missionaries were expelled, and all non-Muslim males in the south between the ages of sixteen and fifty were required to undergo traditional initiation rites known as yondo in order to gain promotion in the civil service and the military. These rites, however, were native to only one of Chad's ethnic groups, Tombalbaye's own Sara people, and even then, only to a subgroup of that people. To everyone else, the rituals were harsh and foreign.
Meanwhile the drought worsened throughout Africa, so in order to improve the dismal economy, people were forced to "volunteer" in a major effort to increase cotton production. With his support in the south diminished, Tombalbaye lashed out at the army, making arbitrary promotions and demotions. Finally, on April 13, 1975, after some of the countries leading officers had been arrested for involvement in an alleged coup, a group of soldiers killed Tombalbaye and installed Félix Malloum, now a general, as the new head of state.