After Abacha's death he was arrested and tried for murder and attempted murder of Kudirat Abiola, wife of the presidential candidate M.K.O. Abiola.
On 30 January 2012, a Lagos High Court sitting at Igbosere convicted Major Hamza Al-Mustapha over the murder of Kudirat Abiola, the wife of the acclaimed winner of the June 12, 1993 Presidential election, Chief Moshood Abiola.
He was also sentenced to death by hanging but was discharged and acquitted of the crime by the appeal court, Lagos division on Friday, July 12, 2013. The appellate court said there was not enough evidence to incriminate Al-Mustapha in the murder of the Late Kudirat Abiola.
Al-Mustapha joined the army and was trained as an intelligence operative. He was involved in at least two investigations of coup attempts. His conduct of interrogations brought him to the attention of Sani Abacha. When Abacha was Chief of Army (August 1985 – August 1990) al-Mustapha was his Aide-de-Camp.
Hamza al-Mustapha was appointed Chief Security Officer to the Head of State (CSOHS) with a Special Strike Force Unit during Abacha's military regime (17 November 1993 – 8 June 1998). Both Ibrahim Babangida and Sani Abacha gave Captain (later Major) Hamza al-Mustapha exceptional power, considerably greater than other officers who were nominally his superior.
After being appointed Chief Security Officer, Al-Mustapha established a number of small security outfits recruited from the military and other security organizations, and trained in Israel and Korea. Abacha's National Security Adviser Ismaila Gwarzo and al-Mustapha were said to be responsible for much of the "torture, killing and wanton looting" during Abacha's rule. On the orders of Sani Abacha's wife Maryam, al-Mustapha detained and tortured several women suspected to be Abacha's girlfriends.
As head of the State Security Service (SSS) al-Mustapha was also said to be involved in drug trafficking, using diplomatic pouches to transport the drugs. His wife, an Arab in origin, coordinated a ring of traffickers in the Gulf states.