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When Mathipa was assigned to the case a month later, he issued a subpoena to special forces to force them to hand over full details of this alleged training exercise and all the personnel involved.
When access to these documents was finally promised, three months later, Mathipa had a premonition that he would be murdered - according to Brig Paulina Sekgobela, his commanding officer.
"When [Mathipa] left my office he said: 'Brigadier, you know, these people - they are going to kill me. I'm going to die'," she told the BBC.
On the day Mathipa was killed, he was phoned by a man calling himself Tebogo, who claimed he had information on the case for the detective - according to Mathipa's daughter Basetsana, who was home with him at the time.
Mathipa and Tebogo arranged to meet at a petrol station in Pretoria.
When Tebogo failed to show, Mathipa drove away again, along the highway.
He was killed while driving, by rounds fired from high-velocity weapons which special forces would have had access to, according to South African police.
And footage from motorway toll gantries, police say, shows one of the occupants of the black BMW, which tailed Mathipa moments before his murder, was Maj Sunnybooi Wambi.
This car, like the three vehicles connected with Abadigga's disappearance at the mall, was registered to PCT, they add.
New detectives were assigned to the case after Mathipa's death, triggering a chilling message from special forces, that made its way to the police's Criminal Intelligence division.
Police say it warned that, however many investigating officers were assigned to the case, "we will kill all of them".
Twelve members of the South African military have been arrested in total, including Lt Col Sunnybooi Wambi, and the current head of South Africa's special forces, Brig Gen Solomon Lechoenyo - both promoted to these positions since police first started investigating their roles in the case.
The 12 have been variously charged with the abduction and murder of Abadigga and Abotese, the murder of Mathipa, fraud, and obstruction.
All deny all charges and they were initially released on bail. But six of them later had their bail revoked, and were ordered to turn themselves in to custody.
Three of the six, including Wambi, have been charged with both Mathipa's murder, and Abotese's abduction and murder.
