President Abdallah was shot to death on the night of November 26-27, reportedly while asleep in his residence, the Beit el Salama (House of Peace). At first his death was seen as a logical outcome of the tense political situation following what was, in effect, his self-appointment as head of state for life. The recently dismissed head of the Comoran military was duly blamed for the murder.

Evidence emerged subsequently that Abdallah's assassination resulted from the late president's proposed actions with regard to the GP [Presidential Guard (Garde Presidentielle--GP)]. In September 1989, Abdallah had engaged a French military consultant, who determined that the GP should be absorbed into the regular army. Following consultations among Abdallah, the French government, and South Africa's Ministry of Foreign Affairs, a decision was made to expel Denard and his fellow officers of the GP by the end of 1989. Denard and his second in command were seen walking with Abdallah only hours before he died. Although the mercenary initially blamed the assassination on the Comoran army, he later conceded that he was in Abdallah's office when the president was killed, but called the shooting "an accident due to the general state of mayhem" in the Beit al Salama.

Two days later, on November 29, the real reasons for the assassination emerged when Denard and the GP seized control of the government in a coup. Twenty-seven police officers were killed, hundreds of people were arrested, and all journalists were confined to their hotels. The mercenaries disarmed the regular army, ousted provisional president Haribon Chebani, who as chief of the Supreme Court had succeeded Abdallah, and installed Mohamed Said Djohar, who just three days earlier had become chief of the Supreme Court, as Comoros' third president in less than a week.

The immediate reaction of the republic's two main supporters, France and South Africa, was to isolate Denard. South Africa, admitting years of funding of the GP, cut off all aid. France began a military build-up on Mahoré and likewise suspended aid. On December 7, anti-Denard demonstrations by about 1,000 students and workers were violently broken up by the protests. By then the islands' school system had shut down, and the civil service had gone on strike. Faced with an untenable situation, Denard surrendered to French forces without a fight on December 15. Along with about two dozen comrades, he was flown to Pretoria and put under house arrest. The French government later announced that Denard would remain in detention in South Africa pending the outcome of a French judicial inquiry into Abdallah's death. In February 1993 he returned to France, where he was initially arrested, tried, and exonerated of involvement in the death of Abdallah.