On 2 October 1995, Muziwendoda Mdluli, NIA chief of security, was found dead in his car in Pretoria from a gunshot wound to his head that would shock the organisation.
[17] Joe Nhlanhla, Minister of Intelligence Services, would also say at the same time that the NIA needed to accelerated its transformation into an institution whose personnel reflect the demographic profile of the country as a whole, united by a commitment to the new, non-racial South Africa and attain "full representativity " in gender, disability and race.
On 18 November 1999, a covert security camera had been found in a waste bin opposite the German Embassy which officials would claim was part of an anti-crime operation and not the monitoring of visitors to the building.
[26] The front companies had been set up in the late 80s by a number of former apartheid South African intelligence officials including Eugene de Kock.
[26] The Scorpions had failed to act on intelligence supplied when in September 2000, the NIA had provide information that Pagad was planning to assassinate a judicial official.
[28] Billy Masetlha was suspended on 22 October 2005 because of allegations that he had conducted illegal intelligence operation against an ANC official and businessman Saki Macozoma, a Mbeki supporter, a potential alternative candidate for president.
[5][29][30] It appeared that a succession battle for the presidency was occurring within the ANC between Thabo Mbeki and Jacob Zuma, with high-ranking civil servants involved.
[29] On 6 November 2005, Gibson Njenje, head of operations of the NIA, who had been suspended because of his illegal surveillance of Saki Macozoma, resigned though he was not involved in the false e-mail issue being investigated by the Inspector General of Intelligence.
[32] With the withdrawal of his legal action against Ronnie Kasrils and the later lifting of his suspension, Njenje had resigned with his pension intact and a settlement package included.
[35] Project Avani initially involved no targeting of individuals but was to evaluate potential threats occurring from the succession battle for the Presidency as well as any foreign interference in it, Zuma's corruption trial, problems from poor service delivery in the townships and lastly the security and stability in the country.
[35] Intelligence Minister Ronnie Kasrils was not aware of the project which appeared legitimate though he should have been informed to provide executive oversight because of the sensitivity of the research.
[35] Ngcakani alleged that the project had been highjacked by Masetlha which involved the telephonic interception of conversations of senior ANC officials, the opposition, businessmen and civil servants as well as surveillance of some people.
[38] By January 2009, Billy Masetlha, IT expert Muziwendoda Kunene and former NIA manager for electronic surveillance Funokwakhe Madlala were acquitted in a Pretoria court of fraud charges relating to hoax emails that implicating senior ANC members in a conspiracy against Jacob Zuma.
[39] On 29 March 2006, President Thabo Mbeki appointed Manala Manzini as director general of the National Intelligence Agency, who'd been the acting head since October 2005 with the suspension and eventual termination of Billy Masetlha's services.
[41] During June 2006, he was part of a delegation including the Intelligence Minister Ronnie Kasrils and the SASS, that visited Zimbabwe and President Robert Mugabe with the aim of kick-starting the South African diplomatic effort to resolve the economic and political issues occurring in that country.
[45] Manzini and police Crime Intelligence Service member Mulangi Mphego managed secured an affidavit from the NPA main witness Glenn Agliotti retracting most of his bribery allegations against Selebi and claimed that Gerrie Nel's Scorpions and the NPA were engaged in a political campaign against Selebi and that their chief witness Aliotti had been threatened and intimidated into making the allegations.
[46] Further investigations by the Mail and Guardian in November 2008 would find that Manzini had conducted business undertakings and a dodgy property deal with Tania Volschenk, Glenn Agliotti's landlady and fixer.
[56] Reason for his 'resignation' concerned issues with Cwele that included political intelligence gathering operations being conducted on senior ANC members and ministers involved in a succession battle in Mangaung.
[57][58] In parliament, Cwele would not be drawn on the reasons for Njenje resignation nor whether Mo Shaik, foreign intelligence branch director and Jeff Maqetuka, State Security Agency director-general would lose their jobs too.
[59] Other reasons mentioned for the breakdown included Cwele's lack of experience and management style in relation to the security environment and intelligence protection for his wife, Sheryl, during her drug-smuggling trial that resulted in her conviction and sentence to 12 years in jail which she would appeal.
Bheki WJ Langa was appointed head of the domestic branch of the State Security Agency on 1 August 2015 filling the post that remained empty since the redeployment of Simon Ntombela in September 2014.