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A few months ago, South Africa recalled its ambassador to Japan. He promptly vanished.

This was no ordinary diplomat. Thulani Dlomo, also known as Silence Dlomo in some of his several diplomatic passports, was one of South Africa’s most powerful spies – and a close ally of former president Jacob Zuma. Today, he still cannot be found, raising more questions about the illicit influence of espionage networks in post-apartheid South Africa.

For five years, until Mr. Zuma rewarded him with a plum appointment to Japan in 2017, Mr. Dlomo had controlled a “special operations” unit at South Africa’s State Security Agency. It became a parallel spy agency, operating in the shadows to serve Mr. Zuma’s personal agenda and defend his political power until he finally resigned from the presidency amid a corruption scandal last year.

Mr. Dlomo’s story – his loyalty to Mr. Zuma’s ambitions, his use of intelligence assets for allegedly illegal action against Mr. Zuma’s critics and his mysterious movements this year – illustrates the covert tactics that have helped leaders of the ruling African National Congress neutralize their opponents for decades.

In a report this year, after a lengthy investigation into the State Security Agency, an official review panel found that Mr. Dlomo’s special operations unit had secretly engaged in a wide range of rogue operations: spying on trade unions and student organizations, covertly monitoring and penetrating South African civil society groups, using disinformation to weaken anti-Zuma protests, targeting Mr. Zuma’s rivals in the ANC, setting up a fake union to undermine a large independent one and “infiltrating and influencing the media” in an attempt to prevent bad publicity for Mr. Zuma.

The special operations unit had become “a law unto itself” and “directly served the political interests” of Mr. Zuma, even providing secret parcels of cash to the intelligence minister and other beneficiaries, the report said. Many of the unit’s intelligence operations were “clearly unconstitutional and illegal.”

The high-level panel, headed by former cabinet minister and anti-apartheid activist Sydney Mufamadi, issued its 106-page report in March. It recommended criminal prosecution of those who had led the illegal activities over the past decade. But most key officials have managed to evade punishment so far – including Mr. Dlomo, who was ordered back from his diplomatic post in January but then vanished.

For months, South Africa’s intelligence agency searched for him, seeking to deliver a dismissal notice. They could not find him, even though he remained on the state payroll until October.

“We dispatched our officials to look for him, and he is nowhere to be found,” State Security Agency official Mahlodi Muofhe told a South African news outlet. “It has taken so long because he’s been evasive.”

At least seven home addresses have been linked to Mr. Dlomo in Durban, the biggest city in Mr. Zuma’s political stronghold, the province of KwaZulu-Natal. But when South African journalists visited the addresses, they found no trace of him.

South Africa has a long history of murky espionage, hidden informants and infiltrators. During the apartheid era, spies were a major weapon in the arsenal of the state, often leading to assassinations or abductions of the regime’s opponents. The ANC, in exile, used espionage as a way of finding targets in the apartheid system – and destroying any internal rivals to its own leaders.

It was from this internal espionage system that Mr. Zuma emerged. He was the ANC’s intelligence chief, specializing in counterintelligence against suspected spies. It fuelled a paranoia and an obsession with security that escalated when he became president in 2009.

Under the first post-apartheid president, Nelson Mandela, in the late 1990s, the South African cabinet did not even include a minister of intelligence. But in the Zuma era, the political use of state espionage assets swiftly escalated. To head the “special operations” unit, Mr. Zuma recruited Mr. Dlomo, who had previously been implicated in a corruption scandal in KwaZulu-Natal.

The State Security Agency began insisting that a growing number of civil servants and even public-health doctors and journalists at the state broadcaster be vetted with “security” clearances. Telephone surveillance became more common and one of Mr. Zuma’s intelligence ministers, David Mahlobo, sometimes boasted to journalists that he had the ability to listen to their calls.

In early 2017, when Mr. Zuma decided to fire his finance minister and deputy finance minister, both of whom had been campaigning against corruption, he cited the findings of an “intelligence report” – which was later found to be bogus.

Later that year, when ANC veteran (and now president) Cyril Ramaphosa challenged Mr. Zuma’s favoured candidate for the ANC leadership, Mr. Ramaphosa’s e-mails were hacked and leaked, revealing details of extramarital affairs.

The e-mails were obtained by “state organs,” Mr. Ramaphosa alleged. South African media reported that Mr. Dlomo’s unit was conducting illegal surveillance on Mr. Ramaphosa and his allies to intercept their phone calls and e-mails.

This year, the independent investigation confirmed that the spy agency was being used in ANC factional battles.

“There has been a serious politicization and factionalization of the intelligence community over the past decade or more, based on factions in the ruling party, resulting in an almost complete disregard for the Constitution, policy, legislation and other prescripts,” the high-level panel said, noting that the State Security Agency had been turned into a “private resource.”

Mr. Zuma continues to battle for influence in the ANC today, and South African media have reported that Mr. Dlomo’s former agents – numbering more than 180 – could still be helping the former president.

In mid-October, in testimony to a parliamentary committee, State Security Minister Ayanda Dlodlo admitted that her attempts to reform the State Security Agency were running into obstacles. The pace of change was “a problem,” she said. “This affects the integrity of the country, it affects the lives of people.”

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