Faced with shrinking popularity and an armed and organized domestic resistance, Siad Barre unleashed a reign of terror against the Majeerteen, the Hawiye, and the Isaaq, carried out by the Red Berets (Duub Cas), a dreaded elite unit recruited from among the president's Mareehaan clansmen. Thus, by the beginning of 1986 Siad Barre's grip on power seemed secure, despite the host of problems facing the regime. The president received a severe blow from an unexpected quarter, however. On the evening of May 23, he was severely injured in an automobile accident. Astonishingly, although at the time he was in his early seventies and suffered from chronic diabetes, Siad Barre recovered sufficiently to resume the reins of government following a month's recuperation. But the accident unleashed a power struggle among senior army commandants, elements of the president's Mareehaan clan, and related factions, whose infighting practically brought the country to a standstill. Broadly, two groups contended for power: a constitutional faction and a clan faction. The constitutional faction was led by the senior vice president, Brigadier General Mahammad Ali Samantar the second vice president, Major General Husseen Kulmiye and generals Ahmad Sulaymaan Abdullah and Ahmad Mahamuud Faarah. The four, together with president Siad Barre, constituted the politburo of the SRSP.

Opposed to the constitutional group were elements from the president's Mareehaan clan, especially members of his immediate family, including his brother, Abdirahmaan Jaama Barre the president's son, Colonel Masleh Siad, and the formidable Mama Khadiija, Siad Barre's senior wife. By some accounts, Mama Khadiija ran her own intelligence network, had well-placed political contacts, and oversaw a large group who had prospered under her patronage.

In November 1986, the dreaded Red Berets unleashed a campaign of terror and intimidation on a frightened citizenry. Meanwhile, the ministries atrophied and the army's officer corps was purged of competent career officers on suspicion of insufficient loyalty to the president. In addition, ministers and bureaucrats plundered what was left of the national treasury after it had been repeatedly skimmed by the top family.

The same month, the SRSP held its third congress. The Central Committee was reshuffled and the president was nominated as the only candidate for another seven-year term. Thus, with a weak opposition divided along clan lines, which he skillfully exploited, Siad Barre seemed invulnerable well into 1988. The regime might have lingered indefinitely but for the wholesale disaffection engendered by the genocidal policies carried out against important lineages of Somali kinship groupings. These actions were waged first against the Majeerteen clan (of the Daarood clan-family), then against the Isaaq clans of the north, and finally against the Hawiye, who occupied the strategic central area of the country, which included the capital. The disaffection of the Hawiye and their subsequent organized armed resistance eventually caused the regime's downfall.