A number of its senior members have resigned since the beginning of the year, evidently as a result of this supposed hidden motive.
This agenda, pursued outside of the commission's mandate to uncover the truth about corruption in the arms deal, is said to have the sole aim of protecting ANC officials and others implicated in the corruption scandal, including President Jacob Zuma.
Commission chairperson Willie Seriti and the man seen as his enforcer at the commission, Fanyana Mdumbe, are described as central to the implementation of the supposed second agenda.
As head of the commission's legal research and Seriti's right-hand man, Mdumbe has strict control over the flow of information, investigations and evidence in the probe. Few members of his team have a handle on exactly what these arms deal investigations entailed, or an overview of what evidence of corruption has been submitted or gathered, according to legal sources.
The unexpected postponement this week of the public hearings until August 19 did not come as a surprise to some sources privy to events, as they believe the "second agenda" will now be implemented, critical documents will be excluded from the process, and evidence will be heard in camera. Witnesses would then be able to avoid answering questions or testifying on matters, with the justification that it is classified, they said.
Seriti granted the postponement on Monday, after lawyers for the defence department said they had been unable to declassify certain documents related to the arms deal.
Former banker Terry Crawford-Browne, who forced Zuma's hand to set up the commission of inquiry by taking him to court, is not surprised by any of the developments and believes there are "multiple agendas at play" at the commission.
"There are multiple agendas, including that the ANC, its officials and Jacob Zuma can never admit that they were conned by European governments and arms companies, and that the arms deal driven by Joe Modise and Thabo Mbeki represented the betrayal of the struggle against apartheid," he said this week.
Tip of the iceberg
Crawford-Browne believes the arms deal was just the tip of the iceberg, leading to many other deals that came with kickbacks. People were deployed to block investigations and prosecution, he said.
"And Judge Willie Seriti and Fanyana Mdumbe were deployed to abort the arms deal investigation when Zuma's legal counsel was unable to refute the mountain of evidence that I presented to the Constitutional Court."
Responding to questions this week, commission spokesperson William Baloyi wrote in a statement to the Mail & Guardian: "We find it strange that some of the people who had been calling for the appointment of a commission to investigate allegations of fraud, corruption etc in the arms-procurement process are now the very people who have been vilifying this commission from its inception and are seeking to discredit it.
"Otherwise, how do you accuse the commission of covering up for ANC leaders and officials when some of them have already been subpoenaed to appear at the public hearings? Or, are these people merely being used by the M&G to further its own campaign to discredit this commission?"
Concern about the alleged second agenda was first raised when the former senior investigator at the commission, Mokgale Norman Moabi, dramatically quit his job in January, citing "a second agenda" driven by Seriti. The judge denied all knowledge of a second agenda and asked Moabi to produce proof.
However, last week, the former principal legal researcher at the commission, attorney Kate Painting, followed suit and publicly broke her silence to reveal to M&G Online that she had resigned in March after a disturbing "second agenda" emerged at the commission.
The resignations snowballed when arms procurement commissioner Judge Francis Legodi quit his job last week on the eve of the commission's public hearings.
The timing of his departure raised many questions. Zuma said he had resigned for "personal, confidential" reasons, but the M&G has been informed he was sidelined by Seriti, but told colleagues he would "go quietly".
On Tuesday, the presidency announced that it had decided not to replace Legodi and it would now only have one commissioner. Seriti would stay on as chairperson, and Justice Thekiso Musi, who was formerly a commissioner, would stay on at the commission as a member. The presidency did an about-turn that same night and said Zuma was still considering the matter.
Mdumbe is something of an enigma at the Arms Procurement Commission (APC). The M&G was informed that when auditor Jabu Mahlangu joined the commission, he asked Mdumbe for all the arms deal documents and evidence in his possession so that he could create an inventory.
"It turned into quite a tiff and [commission secretary] Pretty Luphondo had to intervene, as by law the auditor is allowed access," said a source privy to events.
Baloyi did not respond to questions about this incident.
The M&G informed the commission it was writing about Mdumbe and asked whether he could be interviewed, as previous attempts to talk to him had proved unsuccessful. However, the commission did not respond.
Before moving to his new job in March 2012, Mdumbe worked as a principal state law advisor and researcher at the South African Law Reform Commission. This was where Mdumbe met Seriti, who was its vice-chairperson until the commission's term of office expired in December 2011.
Baloyi described Mdumbe as a "competent, hardworking professional who has been leading the commission's investigations". Others who have worked alongside Mdumbe say his "arrogance" was difficult to handle and they learnt to avoid him.
Moabi highlighted Mdumbe's perplexing role at the commission in his resignation letter. Strict instructions had been given to evidence leaders hired to assist the commission that there was "only one person" to contact in respect of any queries, he said. Baloyi later identified this person as Mdumbe, who is still on secondment from the department of justice.
Mdumbe was leading the commission's investigations, Baloyi said, and was "best suited" to prepare briefs for the evidence leaders.
Moabi claimed in his resignation letter that, as a result of this clandestine operation maintained by Mdumbe and Seriti's "total obsession" with the control of the flow of information to and from the commission, none of the professional staff had any knowledge of what was in the briefs or files that went to the evidence leaders – except "one person".
In his resignation letter, Moabi also alleged that "unknown persons" had dictated what information should go into the legal briefs to evidence leaders and who should deal with which briefs.
There has been criticism that it is extremely unusual for an advocate to be briefing other advocates, in this case the evidence leaders. Baloyi confirmed that Mdumbe had not done his pupillage, but said he did not perform the functions of a practising advocate at the commission.
"His role is that of a researcher and investigator and he is eminently qualified for that in terms of academic background and relevant experience," said Baloyi. "Besides, the commission is not a court of law and is not bound by formalistic rules applicable to the briefing of advocates by attorneys."
Moabi explained that the known agenda was the one defined in the Government Gazette, with clear objectives and stated expectations of what the commission should do and achieve. But, he said: "The second agenda is the real work in progress at the commission that will deliver the report to the president of the Republic of South Africa."
Zuma is not required to make the final report of the commission public. There is now a concern among arms-deal activists about whether Zuma will publish the report and, if he does publish it, whether it will be published in full.
In February this year, Seriti wrote a letter to Crawford-Browne's lawyer claiming he had found no evidence implicating the ANC in corruption. Yet evidence of the bribery by foreign companies of ANC government officials and others in the 1999 arms deal that cost the country up to R70-billion was gathered in abundance by investigators in both Germany and the United Kingdom.
"Currently no evidence implicating the African National Congress has been brought to the attention of the commission," Seriti wrote.
"Should such evidence come to light, the commission will deal with the matter as it deems appropriate. The commission wishes to express its irritation with the persistent allegation by your client and yourselves that evidence leaders are kept in silos, implying that certain information is withheld from them. No evidence leaders are kept in the dark about the activities of the commission."
An intern and recently graduated LLB student at the Institute for Accountability in Southern Africa, Kameel Premhid, went to assist with Crawford-Browne's testimony preparation, as Crawford-Browne was originally scheduled to give evidence at the public hearing in March, before the entire witness list was changed.
"I was briefed to go the commission premises so that I could inspect some of the documents that Terry had been offered inspection of by the commission and in respect of which he had won a high court discovery order years ago," Premhid wrote on the institute's website in May. "The International Offers Negotiating documents (IONT) are the inside working of the government's team that dealt with arms suppliers and ensure that South Africa received the best return for its investment."
Premhid said he was warmly welcomed, even by Mdumbe. Considering what was written about Mdumbe in Moabi's resignation letter, he had expected his interactions with him to "be bruising".
"Mdumbe was most gracious and instructed the APC document managing team to bring me the first two of nine lever arch files groaning under the weight of the IONT correspondence they contained," Premhid wrote.
But when he returned the next morning, the same Mdumbe must have been replaced with "his slightly less accommodating doppelganger".
"After initially bringing all nine files to me, two hours after pouring over the close type-script, Mdumbe burst into the room and summarily informed me that I would not be allowed to read the documents anymore," Premhid wrote. "My shocked expression was given a glib explanation: a decision had been made to limit access based on security concerns and if anything changed, it would be communicated to us in time."
Mdumbe apparently refused to budge on this, and when the director of the Institute for Accountability, Paul Hoffman, and Crawford-Browne arrived, they also made no headway. "It seemed Mdumbe didn't want a fight for our legitimate access to the documents: we were told he had gone to Cape Town," said Premhid.
Only after a threat of urgent legal action did Seriti accede to the requests for access to the documents, but he declined to give them an audience.
While Premhid went off to carry on his studies at Oxford University in the United Kingdom, the commission has battled to regain credibility since Moabi's departure.
Evidence leader Tayob Aboobaker caused another ripple when he submitted his resignation to the commission last week, later retracting it after discussions.
According to the Sunday Times, which saw his resignation letter, he complained of nepotism, lack of professionalism and infighting.
While some of the other evidence leaders and commission staff are known to be demoralised, the one person who appears not to be going anywhere is Mdumbe.