Alex Eliseev: Yet more NPA intrigue

The National Prosecuting Authority (NPA) is due to receive a high-level resignation on Thursday. Breatheā€¦ it's not another National Director of Public Prosecutions (NDPP). Those get fired. This is the departure of suspended head of the Integrity Management Unit, Prince Mokotedi, who says he wants to focus on his church ministry. But, as always, there's a deeper story.

As reindeer herders in remote regions of Siberia discover more alien-looking craters - giant black holes that have appeared, without explanation, above the Arctic circle - South Africa's very own enigma, the NPA, has spat out a fresh mystery.

Prince Mokotedi, the head of the NPA's Integrity Management Unit, is expected to hand in his resignation on Thursday (or at the latest Friday), after around six weeks of being on suspension. Mokotedi says he has been with the NPA for around a decade and his departure is therefore no trivial matter, especially considering his role.

The NPA is not confirming why Mokotedi was suspended, saying it's a private matter. But it's been widely reported that it has to do with a leaked report relating to the organisation's legal battle with prosecutor-turned-politician Glynnis Breytenbach, which we all know is in itself the most complicated story in the history of complicated stories. Mokotedi has denied leaking the report, which accuses Breytenbach of serious misconduct, which she has also denied.

Speaking on Wednesday, Mokotedi made it clear that he planned to leave quietly. There will be no labour disputes or court cases. He will slip away and pursue other interests. He says he is a pastor and the free time he will have will allow him to focus on this. The NPA has confirmed it's been expecting his resignation since last month, following a meeting between Mokotedi and new NPA boss Mxolisi Nxasana, who is himself now the subject of an inquiry into his fitness to hold office.

At the end of June, Mokotedi called into the John Robbie show on Talk Radio 702 and popped open a can of worms. He referred to himself as a so-called "Zuma man" and spoke of factions in the NPA. On Wednesday, he was happy to speak out again, confirming he would be serving his resignation and warning that the internal battles within the NPA would never stop.

Mokotedi identified the epicentre of the 'fault lines': the Jackie Selebi trial at which he testified for the defence (accusing prosecutors of abusing a secret fund) and the disbanding of the Scorpions, which investigated the police chief and sent him to jail for corruption. He made wide allegations that the team involved in that case was still after him and that a senior manager in another unit needed to be removed if the NPA is going to ever 'come right'.

In another interview with The New Age, published on Wednesday, he spoke of 'infighting' and said he was being 'targeted'. He has apparently clashed with Nxasana, who, in turn, referred to Mokotedi as "one of a certain people" who were against his appointment. It's all terribly messy.

Mokotedi says he doesn't want any deals and his will be a 'straight resignation'. The implication of this is that the truth behind his suspension could be buried and the sweeping (but serious) allegations he has made - against highly respected investigators and prosecutors - will go untested. If there was to be a disciplinary hearing, the media may well have succeeded with an application to attend it. If a labour court challenge followed, then the windows would be thrown wide open. But as it stands, South Africans will be left with another dose of controversy and allegations of political interference. Mokotedi's claims are a parting shot which will echo across an organisation which is yet to see an NDPP serve out a full term in office. Nxasana's future is now also uncertain.

The only clarity that has been obtained is why Mokotedi felt bold enough to call into a radio show last month to speak publicly about the NPA's dirty laundry. He knew he was resigning. But his exit leaves even more questions, the biggest one around when some kind of tipping point will be reached? When will the time come for a minister to intervene meaningfully and sweep out persistent claims that the NPA is being weakened by political masters, who have divided it, preventing it from dispensing blind justice?

The NPA and the Justice Department have impressed the world through the handling of the Oscar Pistorius murder trial and the extradition of Shrien Dewani. There are many other cases that run in the background that require devoted prosecutors who secure impressive convictions and justice for victims or their families. Prosecuting a national police commissioner or Radovan Krejcir takes guts and skill. But the crater which has been created around Prince Mokotedi will continue to damage the NPA, sucking in so much of the good work being done around it.

Scientists will no doubt solve the mystery of the Siberian holes. Maybe afterwards, they can swing by Pretoria.

_Alex Eliseev is an Eyewitness News reporter. Follow him on Twitter at _ @alexeliseev

This column first appeared on Daily Maverick.