The Scorpions gained a reputation for investigating and prosecuting high-profile cases, sometimes involving high-ranking politicians of the ruling party, the African National Congress (ANC). Between 20, they initiated 368 investigations, completed 264, and prosecuted 214, with a conviction rate of 85% during that period they also seized R1 billion in assets and contraband worth R1 billion. 349 prosecutions resulted in convictions, representing an average conviction rate of 93.1%. By February 2004, they had completed 653 cases, comprising 273 investigations and 380 prosecutions. However, it was evidently successful, with the Scorpions achieving a conviction rate of over 90% during its tenure. This model has been criticised for undermining "the separation of powers" between investigators and prosecutors. The Scorpions pursued a "prosecution-led" approach or "troika model", meaning that investigators, forensic analysts, and prosecutors worked together on each case – investigators collected evidence for study by analysts, and both were directed by the needs of prosecutors in building a legally strong case. It came to focus on such crimes as drug trafficking white-collar crime in government and the private sector, especially organised corruption and serious and complex financial crime and money laundering and racketeering, especially under the 1998 Prevention of Organised Crime Act.
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Its operational mandate, however, was slightly narrower than its legislative mandate – it was envisaged that the Scorpions would discuss the cases it took on with the Minister and with the police. The unit was governed by the 1998 NPA Act, Section 7 of which gave it extremely broad powers to investigate and prosecute any organised crime or any other crimes determined by presidential proclamation. Though independent, as a unit of the National Prosecuting Authority (NPA) the Scorpions drew their budget through the Ministry of Justice and Constitutional Development and were ultimately subject to the Minister's oversight.
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They were divided into two main directorates: Operations, and Strategic and Investigative Support. Their founding complement was 200 staff and, though this was supposed to expand to about 2,000 staff within two years, they employed only 536 staff at the time of their disbanding. The Scorpions were led by a Deputy Director of Public Prosecutions, a position first held by Frank Dutton (1999–2001) and later by Percy Sonn (2001–2003) and Leonard McCarthy (2003–2008). It was formally disbanded in January 2009 and replaced by the Hawks, a move pushed through Parliament by the ANC and often alleged to have been politically motivated. to deal with all national priority crime, including police corruption." Though formally launched in Gugulethu on 1 September 1999 as the Directorate of Special Investigations, the unit did not legally or operationally come into existence until January 2001, by which time it had been renamed DSO. President Thabo Mbeki announced the establishment of the Scorpions in June 1999, promising "a special and adequately staffed and equipped investigative unit. An independent and multidisciplinary unit with a unique methodology which combined investigation, forensic intelligence, and prosecution, the Scorpions were known as an elite unit, and were involved in several extremely high-profile investigations, especially into the Arms Deal and into high-ranking African National Congress (ANC) politicians including Jackie Selebi, Jacob Zuma, and Tony Yengeni. The Directorate of Special Operations ( DSO), commonly known as the Scorpions, was a specialised unit of the National Prosecuting Authority of South Africa, tasked with investigating and prosecuting high-level and priority crimes including organised crime and corruption.