Magan Isse has been married four times and has five daughters and one son. He had two daughters with his first wife. From his second marriage were born his son Mahad, his activist daughter Ayaan and his daughter Haweya. Haweya died in 1998. He also has a daughter from his third marriage. He later remarried his first wife, who he had divorced shortly after he married his second wife.
He studied in Italy and in the United States at Columbia University, New York (where he got a degree in anthropology). As a linguist and anthropologist he is known as a champion of the Somali script, the so-called Somanya, unlike the former head of state, Siad Barré, who made Latin script the national standard in Somalia in 1970.
In 1976 Magan Isse escaped from prison and fled from Somalia to Saudi Arabia. In the same year, Siad Barré banned all political parties with the exception of the Somali Revolutionary Socialist Party (SRSF), so the SODAF (a forerunner of the SSDF) was founded in exile in Rome. In the following year Magan Isse moved to Ethiopia, where he witnessed the year-long Ogaden War, one of the bloodiest conflicts ever to have happened in Africa. It was also the period of the Red Terror of the Derg, and its victims included the Western Somali Liberation Front, the adversaries of the SSDF. In 1980 Magan Isse chose Nairobi, the capital of Kenya, as a more stable and peaceful residence for his family, while he continued to live in Somalia and Ethiopia most of the time.
In the summer of 1982 the SSDF played a key role in the second armed conflict between Somalia and Ethiopia. The SSDF, supported by Mengistu's air force, waged a low intensity guerilla war against the Somali army. Magan Isse became a well-known figure in Somalia at the time as director and presenter of Radio Kulmis (meaning "Unity" in Somali), which aired anti-Barré programs from Addis Abeba, Ethiopia).
In 1988, Magan Isse and Mohamed Haji Aden headed an insurrection near Eyl in the Nugaal region, part of Puntland, mainly inhabited by Majerteen of the Issa Mahamoud sub-clans. This insurrection of the SSDF, which started in the southern part of Nugal and Bari and the western part of Mudug, would eventually lead to the autonomy of the province of Puntland in 1998. In the 1990s the SSDF switched sides: from the SNM of Somaliland to its former adversary, Mohammed Said Hersi Morgan, former minister of defense of the government of Siad Barré, and, after the fall of Barré, head of the Somali National Front (SNF). With the SNF the SSDF tried, in vain, to capture the region around Kismayu.