Magan co-founded the Somali Salvation Democratic Front (SSDF), a political and paramilitary group that opposed the government's authoritarian policies, and he was imprisoned for his dissent.

[2] Magan was a comrade-in-arms of erstwhile president of Somalia Abdullahi Yusuf Ahmed, and the father of the former Dutch MP and critic of Islam Ayaan Hirsi Ali.

For security purposes, Magan Isse opted to relocate his family to a suburb in Nairobi, while he continued to live in Somalia and Ethiopia most of the time.

The SSDF, supported by the Derg leader Mengistu's air force, waged a low intensity guerrilla 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 Majeerteen of the Issa Mahamoud sub-clans.